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Friday, December 15, 2017

Watch the red arrows naysayers


Here's a map from yesterday's presentation by Italian archaeologist Massimo Vidale at the MPI-SHH Jena Cross Roads conference on South Asia. He was focusing on the skeletal remains from the protohistoric, and likely early Indo-Aryan, cemeteries at Udegram and Gogdara in the Swat Valley, modern-day Pakistan. Source: Twitter.


And this is my own map from back in August (see here) summarizing what ancient DNA (both published and otherwise...nudge, nudge) is telling us about the early Indo-European, including Indo-Aryan, expansions across Eurasia.


Remarkably similar, aren't they? And obviously I'm not just talking about the use of ellipses and red arrows by the authors of both maps (probably a coincidence, but perhaps not if Prof. Vidale reads this blog).

Keep in mind also that last year Prof. Vidale sent samples from the Swat Valley cemeteries to the ancient DNA lab at Harvard for testing and analysis (see here). So if these samples yielded endogenous DNA (wink, wink), then he probably knew the results when he drew up his map.

See also...

Best of Davidski on South Asian population history

The beast among Y-haplogroups

Descendants of ancient European (fair?) maidens in Central Asia's highlands

198 comments:

Samuel Andrews said...

I expect the early Aryans in South Asia to be something like Andronovo minus possible South Asian admixture.

We have such poor ancient references for South Asians that I'm not convinced we can conclude whether they have EEF admixture or not. If they do it would be so so watered down that the wrong ancient references could hide it.

How do we recouncile R1a M417 in 3500 BC with EEF admixture, R1a Z93 in 2800 BC with EEF admixture, but no EEF admixture in the R1a Z93 rich Aryans? Just doesn't make sense. You got to think all early Indo Iranian communities descended from the same ancestral population. So we expect the Aryans to be similar to Andronovo.

Ric Hern said...

@ Davidski

Thanks.

Where precisely is that red circle at the top situated ? Did that two migrations kick of at the same place, time and Culture ?

Shahanshah of Persia said...

Yes, it certainly looks like the correct route, and therefore, they must have passed through BMAC, undoubtedly. Now, the only question is, how much BMAC DNA did they pick up? I would assume perhaps 10% to 30%. Any thoughts, David? It obviously cannot be more than 30%, though, IMO.

Here: https://upload.wikimedia.org/wikipedia/commons/thumb/b/b8/Indo-Iranian_origins.png/300px-Indo-Iranian_origins.png

The range looks good: http://www.cais-soas.com/CAIS/Images2/Maps/BMAC_Map.png

This is my hypothetical analysis: https://i.imgur.com/PhkGJWc.jpg

I do, however, doubt that the overall impact was major, considering that the EEF impact on the Yamnaya in Europe was also limited. Also, why are your comments now moderated?

Shahanshah of Persia said...

Thanks for this, by the way, David. Much appreciated! :)

Salden said...

>MPI-SHH Jena Cross Roads conference

When was that?

Davidski said...

@All

Sorry, can't get into any discussions right now. You have to help out each other with the questions.

Comment moderation will be on most of the month.

Shahanshah of Persia said...

@Davidski Alright, thanks bro! Best wishes for the holidays. I hope you enjoy your vacation.

Rob said...


The circle looks like the start/ end of the IAMC to me
Also,?some kind of pastoralists moved about the Gujarat as early as the Classic IVC period

Matt said...

Not a naysayer on Indo-European migration to India but have to say, as a map it doesn't tell me too much though too clearly. Looks like some kind of migration from eastern Turkmenistan to Afghanistan and Pakistan into the Swat Cemetary*, Pirak**, Cemetary H*** and I would guess PGW culture.

But as a screenshot and map it is not telling us really whether these are offspring cultures, or cultures which saw influence (or how much on a sliding scale).

I would guess the yellow cultures are hybrids (or show signs of interaction) while the white Ochre Painted Ware+Copper Hoards is a "substrate" that is not Indo-European (or else is of uncertain affilitation?). Or possibly the colour schema is depicting something else? It can't be date order (red>yellow>white) as PGW is I believe younger than OCP.

*https://tribune.com.pk/story/466048/a-lost-civilisation-3000-year-old-cemetery-discovered-in-swat/ - "no weapons were found from the site, unlike most civilisations,” Vidale said". How odd?

** https://en.wikipedia.org/wiki/Pirak - "The historical importance of this site in the South Asia is because of its very early horse remains. Also, the site has some very early ironwork and iron artefacts. The ironwork seems to have had a gradual introduction"

*** https://en.wikipedia.org/wiki/Cemetery_H_culture

Matt Thomas said...

I don't think most of the south asian input is from Andronovo. I think most of it is from Afnasievo.

Chad Rohlfsen said...

The program

http://www.shh.mpg.de/740868/s_asia_workshop_schedule.pdf

Rob said...

Well this featured talk isn't directly genetics based so it might represent the speakers view on various other factors, incl genetics to date


Davidski said...

As I said in the post, however, the speaker sent bone samples from the Swat Valley cemeteries to the Reich Lab last year.

Rob said...

Ah i missed that, T.Y

This slide was interesting too. https://imgur.com/a/GEeqp

Implies ASi moved from south to north ? Very ancient presence

Balaji said...

Prof. Vidale with his map and arrows was no doubt trying to connect his archaeological findings with those of the late Prof. Kuzmina's of the Andronovo. Prof. Reich, too, had a similar map with arrows. But facts are stubborn things. They don't always agree with preconceived notions. Hence the delay in the publication of the aDNA from Swat Valley.

Davidski said...

@Balaji

Here's a better theory: the reason the South Asian paper is taking so long is because some Indian scientists were expecting ancient DNA from South Asia to reflect OIT, but it reflects AIT, so they keep asking for more data because they can't believe what they're seeing.

Apóstolos said...

What is the date R1a1-Z93 should appear in India (or Pakistan?, where exactly?) in order to prove 'AIT' correct in your opinion?

Shahanshah of Persia said...

@Davidski Just ignore him, bro. Indian Nationalists need to admit and accept the hard truths of the Aryan Invasion Theory. It is undeniable now. The only question remaining is the BMAC question, but even then we do not know how BMACized these Aryans were. If they were not BMACized, I would assume that they were similar to Yamnaya, but if they were BMACized, then they were likely a Sintashta/Andronovo-BMAC hybridization.

Davidski said...

@Apóstolos

AIT, or at the very least AMT, is proven when the ancient DNA from South Asia shows that Yamnaya-related peoples started streaming into the region just before or even after the collapse of the Indus Valley Civilization.

So R1a-Z93 should appear in South Asia at the same time as Yamnaya-related ancestry from the steppe, and only become relatively common there during the final phase of the Indus Valley Civilization, or even after its collapse.

Just common sense.

Shahanshah of Persia said...

@Davidski Couldn't they just have been Andronovo/Sintashta peoples? Don't South Asians from upper castes get around 20 to 25% Andronovo/Sintashta anyway? I know, as you know, the average Yamnaya for upper castes is around 36 to 43, in South Asia. Because, it seems unlikely to me that they are Yamnaya derived, since we know that the Yamnaya carried Y-DNA R1b, not R1a.

Anthro Survey said...

@Samuel and Shahanshah

This is the best model I was able to obtain, to date, for Uttari Brahmins using only Paniyas, Pulliyars, and Onge as ASI-rich stand-ins as well as a battery of relevant W_Eurasian individual samples. The samples it "took" for the fit are shown with sample IDs; the ones which it didn't are summarized as categories.

I agree----the EEF probably got watered down along the way. My guess, judging by Yamnaya+Samara_Eneo in the model, is by admixture with some ANE-rich Kelteminar(?) people they would have encountered north of the Zarafshan river. Needless to say, we don't have any Kelteminar DNA, atm. :-(

As for mixing with BMACs?
The jury is very much out. If BMACs resulted from a westward demic expansion from Iran, then no. Otherwise, we'd see more of an EEF-related signal in upper-caste North Indians much like we do in Pahstuns and Baloch---be it in ADMIXTURE or nMonte. Hard to hide two sources of EEF.

Now, if BMACs lacked EEF-related ancestry and were Iran_N-like, then we really can't be certain, but if David Anthony is correct in his thinking about extensive BMAC vocabulary and religious motifs in Sanskrit/Hinduism, this was not unlikely.
(No, we can't just assume sample Iran_N:1945 represents BMAC here because pre-Aryan india could have been Pulliyar+extra Iran_N)


[1] "distance%=0.681 / distance=0.00681"

Brahmin_UP

Pulliyar 58.40
Iran_N:I1945 17.45
Yamnaya_Samara:I0357 13.80
Samara_Eneolithic:I0434 7.15
Yamnaya_Samara:I0441 3.20
Samara_Eneolithic 0.00
Srubnaya 0.00
Poltavka 0.00
Latvia_MN 0.00
Corded_Ware_Estonia 0.00
Yamnaya_Kalmykia 0.00
Yamnaya_Samara 0.00
Sintashta 0.00
Andronovo 0.00
Iran_ChL 0.00
Barcin_N 0.00
Tepecik_Ciftlik_N 0.00
Iran_N 0.00
Paniya 0.00
Onge 0.00
Aeta 0.00

Bronze said...

@Shahansha of Persia

The aryan invasion theory its not confirmed at all, regardless what you say. Even if aryans came from Yamnaya region. Either way Yamnaya is not the same as modern europeans and did not look the same as them. Indians do not have EEF in any meaningful degree which means if the Aryans came from that region they did not resemble europeans.

Chad Rohlfsen said...

This is blog-worthy. I've got these Denisovan traits too. Just found out through Insitome. Great product and worth the money for those interested in archaic and metabolic traits.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5430617/#!po=75.8475

Chetan Vit said...

@Davidski Will the full presentation be available?

Shahanshah of Persia said...

@davidski David, do you know Genetiker? I know this is a tad bit off-topic, but recently he has done some nice analysis of ancient Neolithic genomes in Europe, in terms of their skin color, phenotype, etc. How reliable is he as a genetic blogger? Thanks, mate. Just thought it's something you'd find interesting.

Seinundzeit said...

Sam,

"How do we recouncile R1a M417 in 3500 BC with EEF admixture, R1a Z93 in 2800 BC with EEF admixture, but no EEF admixture in the R1a Z93 rich Aryans? Just doesn't make sense. You got to think all early Indo Iranian communities descended from the same ancestral population. So we expect the Aryans to be similar to Andronovo."

A very sensible point.

With that being said, nearly every method shows the opposite; whether it be PCA-based admixture estimation, ADMIXTURE, most models involving qpAdm, modelling with qpGraph, models based on D-Stat nMonte sheets, and even models based on Matt's Fst PCoA technique.

I have no set views on this matter (waiting for the Swat valley aDNA); but my bet is on substantial Steppe_EMBA-related ancestry (more like Srubnaya_outlier, rather than Yamnaya/Afanesevo) in southern Central Asia and northern South Asia.

For what it's worth, one can exclude Steppe_EMBA, and see how South Central Asians stack-up.

This is what one gets:

Kalash

39.3% Steppe_MLBA + 14.4% CHG + 6.1% AG3-MA1
19.2% Iran_Neolithic + 10.2% Iran_Chalcolithic

10.8% ASI

"distance%=5.791 / distance=0.05791"

As one would expect. The Steppe_MLBA + CHG + ANE combination is highly suggestive of something Steppe_EMBA-related.

Davidski said...

@Bronze

You're exaggerating and you're obviously confused.

The currently available Yamnaya samples cluster more or less with modern-day Europeans on global and Eurasian PCA plots, and this alone is proof enough that overall they couldn't have differed significantly in terms of looks from modern-day Europeans. That they may have differed significantly in terms of a few traits shouldn't be emphasized too much.

And keep in mind that other Bronze Age steppe peoples were even more similar to modern-day Europeans than Yamnaya. So it's possible that the steppe groups that moved into South Asia looked very European indeed, even if they weren't mostly very fair and blond.

@Shahanshah of Persia

But obviously Andronovo and Sintashta are Yamnaya-related too.

Right now, I think that the steppe-derived population that made the biggest impact on South Asian genetics was generally most similar to the Sarmatians from Pokrovka out of all of the currently available steppe samples. But we'll see if that's true when the ancient genomes from South Asia are finally published.

As for Genetiker, he's very hit and miss. In fact, when he misses it's by miles. Let's leave it at that.

@Chetan Vit

All that I know and/or can share with you about this is in the blog post and links.

Shahanshah of Persia said...

@Anthro Survey

I actually have reason to believe that the BMAC peoples were Neolithic Iranian. For instance, David did these for another blogger (can't recall his name):

Iranian_Lor
Iran_Chalcolithic 0.723 ± 0.078
Iran_Neolithic 0.106 ± 0.079
Yamnaya_Samara 0.130 ± 0.024
Han 0.041 ± 0.011

Iranian_Mazandarani
Iran_Chalcolithic 0.558 ± 0.066
Iran_Neolithic 0.209 ± 0.065
Yamnaya_Samara 0.178 ± 0.022
Han 0.055 ± 0.010

Iranian_Persian
Iran_Chalcolithic 0.617 ± 0.064
Iran_Neolithic 0.181 ± 0.062
Yamnaya_Samara 0.148 ± 0.022
Han 0.054 ± 0.010

Kurd_Feyli
Iran_Chalcolithic 0.707 ± 0.070
Iran_Neolithic 0.125 ± 0.072
Yamnaya_Samara 0.139 ± 0.023
Han 0.029 ± 0.011

Kurd_Feyli
Iran_Chalcolithic 0.615 ± 0.070
Iran_Neolithic 0.174 ± 0.066
Andronovo 0.185 ± 0.028
Han 0.026 ± 0.011

Kurd_Feyli
Iran_Chalcolithic 0.626 ± 0.066
Iran_Neolithic 0.138 ± 0.062
Sintashta 0.191 ± 0.030
Han 0.045 ± 0.010

Notice how the Steppe admixture is accompanied by an equivalent amount of Neolithic Iranian DNA. Now, where could that have come from? My best guess is from BMACization in Central Asia, though, again we cannot be certain. Anyway, what made you conclude that BMAC were not Neolithic Iranians because the explanation you offered seem to contradict your conclusion, there.

Anyway, your modelling is a bit off. That was actually one of the not-so-great models I saw for any population. :)

@Bronze

It is 90% confirmed at this point. All you can do now is hope and pray that some BMACization took place in Central Asia. But even then, the original Aryans would be similar to Tajiks and Yaghnobis, not Indians.

@Davidski

Alright, thanks for clarifying, appreciate it. Though, I was wondering, if they were similar to Sarmatians, wouldn't it mean that they had some non-Steppe admixture? Since, you modeled Sarmatians as 60% Steppe at the most. Where did this non-Steppe come from? Europe or Iran/Central Asia?


Salden said...

>The aryan invasion theory its not confirmed at all, regardless what you say.

Yeah it is. Or did the R1a just get to South Asia by magic?

> Either way Yamnaya is not the same as modern europeans and did not look the same as them

Show a single reliable PCA where Yamnaya and similiar groups don't cluster nearest towards Northern to Eastern Europeans out of all modern populations. And how did they look different from modern Europeans? What, do you think all Euros look like Brad Pitt or something? Have you seen any Greeks or Southern Italians?

Salden said...

Genetiker is a White Nationalist who claims that Ancient White Men invented Mesoamerican civilization.

Davidski said...

@Shahanshah of Persia

Since, you modeled Sarmatians as 60% Steppe at the most. Where did this non-Steppe come from? Europe or Iran/Central Asia?

Not sure where you got the 60% from? If from the Steppe K7 analysis, then keep in mind that not even most Yamnaya are 100% "steppe" in that test. The Pokrovka Sarmatians are in fact 75-80% Yamnaya.

Iron Age nomads vs Bronze Age herders: Sarmatians and Yamnaya in qpGraph

The 20-25% non-Yamnaya ancestry proportions are from the steppe as well. They entered the steppe one way or another, like CHG and EEF did at some point.

Davidski said...

@All

Stupid post from Rami removed. He thinks that Yamnaya don't cluster more or less with modern-day Europeans on global and Eurasian PCA plots. As if Eastern (inc. Volga-Ural) Europeans weren't Europeans.

Idiot.

Shahanshah of Persia said...

@Davidski Thanks for clarifying, and yeah, I was looking at the K7. Okay, so the results in the K7 are not accurate? I remember seeing that they had around 8 to 13% Neolithic Iranian DNA. Was this just "background noise"?

Wait, so are the proportions for Northern Europeans in that wrong as well? If so, how Steppe derived are Nordics?

To be fair to Rami, in your PCA, the Yamnaya Samara do form their own cluster, just above Northern Europeans, albeit very closely. Though, they do indeed cluster with Volga Europeans. Are those Volga Europeans Chuvash and Volga Tatars?

So, are you suggesting that the Aryans had no BMAC DNA, at all? Or what? What happened to the BMAC DNA, since we have evidence for some mingling: http://www.people.fas.harvard.edu/~witzel/Sinttashta_Qu.pdf

Like, I don't think all of that BMAC DNA can just disappear or not appear be admixed into the Indo-Europeans who entered India. Unless, of course, the Steppe admixture in India predates BMAC. Any thoughts?

@Salden They cluster the closest to Volga populations, not Nordics, but are nonetheless close to Nordics. On a side note, Genetiker also considers all ancient Caucasoids to be White, which is weird. He also messes with results, often, and his calculations for Steppe populations are a bit odd to say the least. Though, I do like his phenotype analyses. Any thoughts on his other work?

mzp1 said...

Davidski, I don't get it. Udegram is an iron age site. It is far removed from any proposed indo aryan invasion, has no affinities to early rigvedic society and therefore cannot be 'early aryan'.

The level of discussion here needs raising.

Davidski said...

@mzp1

Seems like you're confusing early with proto? Either that or you're just being nitpicky.

Considering what's been published about the Bronze and Iron Age Swat Valley sites, I think it's fair to speculate that they may have belonged to early, as in not modern, Indo-Aryans. It wouldn't be the first time, and your opinion on the matter isn't final, if that's what you think.

Davidski said...

@Shahanshah of Persia

In the two most significant PCA dimensions on the usual West Eurasian plot, Yamnaya samples cluster closest to Russians from the Volga-Ural and Mordovians, also from the Volga-Ural, and they show the lowest Fst distances to these groups as well out of all modern-day populations. On the usual global plots, Yamnaya also cluster with various Eastern European populations.

But of course, Yamnaya Kalmykia/Samara aren't the only steppe groups to consider in all of this. For example, how did that Eneolithic guy with R1a-M417 look like, since he was even more similar to modern-day Europeans than Yamnaya, with a big chunk of EEF?

I think you can figure out the answers to your other questions.

Chetan Vit said...

Probably they already have the R1a z93 samples with the steppe admixture. But when the results are published, it will become clear what kind of steppe admixture it was. Andronovo or Poltavka / Late Yamnaya. Maybe some BMAC and ASI admixture as well.

Rob said...

Yamnaya don't plot with any Europeans , unless you count Russian Tartars as "Europeans".

Chetan Vit said...

@mzp1 Conventional date for Indo-Aryan entry into the subcontinent (1800 BC) is too early and is in need of reconsideration. It would make a lot of sense if it happened after 1500 BC (LBA - EIA), if the said Aryans were part of the Andronovo expansion The Mittani Aryan language which is a little older than the language of the Rig Veda is dated to only 1400 BC. But if they were a late Yamna group, the dates could be pushed back further.

Shahanshah of Persia said...

@Davidski Alright thanks, you've made a good point. I am still confused about the BMAC thing, sorry I am new to this. And I think I remember seeing a comment from you beforehand in another blog entry where you admitted that there was some BMAC admixture, it was around this time last year.

@Rob Well, they are Europeans, to be fair.

Seinundzeit said...

I'm bored, so let me have some fun...

In my estimation, famous American actor Charles Bronson is a rare example of a living person who partakes of the general Steppe_EMBA phenotype:

http://images03.military.com/sites/default/files/media/veteran-jobs/content-images/2012/07/charles_bronson.jpg

We'll say that this Toda man represents Iran_N:

http://files.abovetopsecret.com/files/img/bs525682ea.JPG

This Iranian man will represent Iran_Chl:

http://l7.alamy.com/zooms/43e109b289bb4b54bd6ee76636eb7945/young-iranian-man-at-takht-e-soleiman-in-iran-b377xa.jpg

You combine these in different proportions, and you get various sorts of South Central Asian phenotypes:

http://c8.alamy.com/comp/CY7ECE/kalash-men-with-characteristic-feather-in-their-caps-at-the-joshi-CY7ECE.jpg

http://c8.alamy.com/comp/CXNJ62/elder-kalash-men-listening-to-stories-and-songs-of-the-history-of-CXNJ62.jpg

http://4.bp.blogspot.com/_zbQFuOgH3q4/RhCfQYcMqmI/AAAAAAAADEk/ObfFvtV3CLk/s400/Massoud+Celebration+Sept06+bt+FW+(12).jpg

https://www.icrc.org/eng/assets/images/photos/2014/afghanistan-panjshir-feature-panjshir-001a.jpg

https://rrmackenzie.files.wordpress.com/2014/07/01-dr-h-asm-sitting.jpg

http://blogs.reuters.com/pakistan/files/2011/11/tribesmen.jpg

https://c.tribune.com.pk/2011/09/246867-Talibanphotoexpress-1315340964-335-640x480.jpg

https://www.veteranstoday.com/wp-content/uploads/2013/08/pashtun-males.jpeg

Indian phenotypes would only entail Toda man + Charles Bronson, since unlike South Central Asians they don't have much Iran_Chal (represented by our random Iranian dude).

Also, proper South Asians have enough ASI to affect their facial features.

We'll represent ASI with these South Indian tribal individuals from the early 20th century:

https://qph.ec.quoracdn.net/main-qimg-bb725d65eb0e6cafe99aca03c83b0148

So, you combine Toda man, with some minor/moderate Charles Bronson, and a noticeable amount of the ASI phenotype displayed above, and voila, you get the classic South Asian phenotype:

http://i.dailymail.co.uk/i/pix/2013/04/21/article-2312612-196B9988000005DC-0_634x459.jpg

(Lol)

I'm just kidding people (again, I'm bored)...

In all seriousness, we don't really have a great handle on how ancient people looked.

I mean, we're talking about thousands of years of genetic drift, natural selection, the slow melding of distinct genetic streams, and plain old variability, so can't infer anything from looking at modern Europeans, West Asians, Central Asians, and South Asians. It's a fool's errand.

Anyway, who really cares. The genetic data is much more interesting.

Regardless, shifting gears, arguing against AIT/AMT involves a total disregard of reality.

The Indo-Iranian languages are intrusive to West Asia, South Central Asia, and South Asia. Simple as that.

And, as per the current data, the spread of these languages involved considerable gene-flow, as shown by R1a-Z93, certain shared mtDNA lineages between Europeans and Central/South Asians, and the intense/substantive autosomal signal seen with every analysis.

That's all. Only the details are fuzzy.

Salden said...

>Yamnaya don't plot with any Europeans, unless you count Russian Tartars as "Europeans".

I'm sure you have the reliable PCAs to show that.

Davidski said...

@Rob

Tatars from the Volga-Ural are Europeans, and so are Mordovians. They're certainly not Asians. You can see where the genetic border between Europe and Asia is here (hint: Urals)...

https://www.biorxiv.org/content/early/2017/12/13/233486.full.pdf

And the R1a-M417 Eneolithic steppe sample plots west of Yamnaya, probably with modern-day Ukrainians, so he's very European indeed.

But this is all semantics and not very interesting.

Anthro Survey said...

@Shahanshah

How am I 'concluding' that BMAC wasn't Iran_N when I clearly preface that paragraph with "the jury is still out" and actually lean a bit towards the Iran_N scenario in my mention of David Anthony's argument(s)?

With regards to the models you've posted(generated with a different software than mine, btw): If we make a valid assumption that all this Iran_N was accompanied by steppe, we still don't know what, if any, fraction of "Iran_Chl" percentage was likewise accompanied by these waves into the western plateau. (In other words, BMAC could have sat on a continuum between Iran_N & Iran_Chl for all we know).

As a side note: we also don't know how the fraction of steppe in Iran migrating from Yaz area(r1a-z93) compared to that which crossed the Caucasus(presumably associated with R1b-L23) and what the latter was accompanied by.

With the software I've used(or most others, for that matter) decent fits(<1) for Indians are more difficult to obtain that for Iranians because we don't have satisfactory ASI or ASI-rich proxies atm. Pulliyars, Paniya and Onge are all spatially and temporally distant(the only modern populations I've had no choice but to use) from the ASI-rich populations with whom steppe invaders would have initially hybridized. Although it doesn't directly account for alleles like formal methods, the fits are not gonna be stellar if the standin and the true population have a large drift length.

Davidski said...

@Rob

These have never been part of "Europe"

Eurasia west of the Urals is Europe, geographically and genetically.

Rob said...


Yamnaya was 75% non north-west euraisan, originally.
The Volga bend was Turkic until recently

You're taking great "liberties" to define what European is wrt Yamnaya, which obviously resonates with the likes of Salden, Chetan and Shahna..

Davidski said...

@Rob

Facts...

- the Yamnaya horizon was located entirely in what is now known as Europe

- in terms of modern day affinities, Yamnaya samples cluster with what are regarded as Eastern Europeans

- in terms of modern day affinities, Yamnaya samples share the highest genetic drift and hence genetic history with Northern and Eastern Europeans

- ergo it's fair to describe Yamnaya as European

Of course, you're free to describe Yamnaya in any way you wish, but you shouldn't expect me or anyone else here to agree with you just because.

Anthro Survey said...

I actually have to second Rob here.

Geographically, we can call it Europe, but it's not so clear-cut genetically. I would personally refrain from putting them under "European", "Asian", "Turkic" or "Iranic" umbrellas because they sorta stand alone and fit none too well if we consider modern genetic variation.

Yes, they sit next to some Russians on a 2D PCA, but have a significantly different population history. Run-of-the-mill western Russians result from an eastward expansion out of some "Lusatian horizon" area during the early medieval era.

Tatars, on the whole are essentially a mix of mildly EEF-shifted steppe-rich groups, possibly resident there since 2000BC, with additional Siberian admixture(gotten via some steppe-Siberian Turkic-speaking hybrids?). Even if we ignore the latter, the former is enough to pull them apart from proper northern European groups.

Then, there is the cultural aspect, i.e. gap. Ancestors of groups like Volga Bulgars(ancestral to Tatars) or Iron Age Scythians have been living on the steppe for 2-3 millenia. Offshoots of Unetice, Beakers, Urnfields, etc. like Celts, Germanic and Slavs significantly hybridized with EEFs on much different terrain and their "steppe" portion has led a completely different lifestyle in those same 2-3 millenia. The Urnfield, LaTene, Haltatt, etc. warrior cult phenomena widespread across Europe was absent east of the Dnieper.

In fact, we can argue that Sardinians, another group outside modern genetic variation, are culturally closer to Europe than are Volga Tatars---even if we ignore the Turkic element. That's because Sards have been colonized by Unetice(?) beneficiaries from Italy and maintained close ties to the continent ever since.

Davidski said...

@Anthro Survey

Which Asians, Turkics or Iranics share more genetic drift (ancestry) with Yamnaya than Northern/Eastern Europeans do?

Feel free to list them here.

And I won't even mention again the steppe samples from west of Kalmykia/Samara, which are even more similar to Northern/Eastern Europeans.

Anonymous said...

The proto-Indo-Aryans who brought R1a-z93 to south Asia would have phenotypically resembled the Kalash/Nuristani of northern Pakistan and Afghanistan and other related Dardic people of that region rather than any Europeans proper.

Salden said...

>The proto-Indo-Aryans who brought R1a-z93 to south Asia would have phenotypically resembled the Kalash/Nuristani of northern Pakistan and Afghanistan and other related Dardic people of that region rather than any Europeans proper.

You can show that from clustering?

Davidski said...

@adinke

The proto-Indo-Aryans who brought R1a-z93 to south Asia would have phenotypically resembled the Kalash/Nuristani of northern Pakistan and Afghanistan and other related Dardic people of that region rather than any Europeans proper.

I seriously doubt that if the Proto-Aryan homeland was on the North Pontic steppe, as is generally assumed.

Anthro Survey said...

@Davidski

Actually, various eastern Iranians and Dardics have a fair amount of Yamnaya-related ancestry, too. Modern Europeans are not alone among modern populations in this regard.

Now, Yamnaya and other ancient steppe populations ancestral to Tatars and Europeans are one thing. Modern Tatars and Europeans are another.

If we compare drift between steppe-rich populations ANCESTRAL TO modern Europeans and modern Tatars (~2500-2000BC) there is not gonna be a whole lot of drift.

But, even if we restrict ourselves to the steppe-rich portions of modern Tatars and, say, Swedes, ignoring additional Siberian and EEF admixture, mind you, there is going to be much more(all those millenia elapsed).
It's like comparing Sardinians to the EEF fraction of MODERN Germans(or to a hypothetical northern analogue to Sardinians---like a GlobAmph offshoot).

https://justpaste.it/1enj0 (colored lines are drift path lengths between groups; black lines indicate drift over time and/or admixture; notice that green is much longer than the other two).

Davidski said...

@Anthro Survey

Overall shared drift, as measured with f3 and other formal stats, is a chunky method to measure affinity, but in this case it's rather useful, because it measures all drift paths, going back a long time.

And in this context, (eastern) Yamnaya easily shares most drift with modern-day Europeans from across Northern Europe, west to east. So not only is it an ancient population that comes from a horizon within the modern-day borders of Europe, but it also shares most genetic drift with modern-day Europeans.

So it can be described as a European population. Reasonable people without any agendas should be able to accept this without too much of a problem, no?

Anonymous said...

@Davidski I was specifically talking about the proto-Indo-Aryans who entered south Asia after absorbing admixture from BMAC and whose remains are likely in the Swat/Gandhara grave culture, not about proto-IE or Yamnaya itself.

Btw, what about North Caucasians (Chechens, Lezgins etc.) who are geographically quite close to Yamnaya and have a large amount of steppe admixture. Don't they genetically cluster close to Yamnaya?

@Salden Not until the Swat Valley paper is released, no.

Anthro Survey said...

Complete picture(albeit rushed)
https://justpaste.it/1enjh

Davidski said...

@Anthro Survey

I reckon I've got a better picture here...

https://drive.google.com/file/d/0B9o3EYTdM8lQelZhUGYtN1g1VnM/view?usp=sharing

Davidski said...

@adinke

Btw, what about North Caucasians (Chechens, Lezgins etc.) who are geographically quite close to Yamnaya and have a large amount of steppe admixture. Don't they genetically cluster close to Yamnaya?

They're close, but not closer than Northern/Eastern Europeans, not in terms of PCA, like the one at the link I posted above, or overall shared drift/ancestry.

Yamnaya has a lot of European hunter-gatherer ancestry, as much as modern-day Northern Europeans, if not more, and this means that it's going to be attracted to Northern Europeans when all drift paths are taken into account.

Anthro Survey said...

@Davidski

How does it work out that modern Swedes and Spaniards share more drift with Yamnaya than Yaghnobis and Brahmins do, respectively? Shouldn't it be pretty comparable?

Or, do you mean that if we further extend our branches from yamnaya "downward" towards EHG", we'll get more overall sharing on the account of EHG and WHG(which Europeans do have quite a bit of) ultimately sharing common nodes and drift?

Rob said...

Whatever, its heuristics, but your argument is based on the fact that modern Europeans derive ancestry from Yamnaya to argue Yamnaya is 'European', when in fact a large chunk of its ancestry arrived to Europe in the (i) Early Mesolithic from Siberia (ii) Late Neolithic (from somewhere ? northwest Asia).
The only, arguably, 'European' component in modern Europeans is proto-WHG.

Matt said...

Agree seems like a low level discussion. Still... It's probably about as reasonable to call the Yamnaya Europeans as the Anatolians. It's pretty clear how the patterns of relatedness fit for anyone interested: Yamnaya most related to Europeans; not particularly very related to Europeans (compared to, say, EEF), lowest Fst distance from Yamnaya is to Tabasaran, then Komi=Erzya=Lezgin=Moksha=Russian=Tajik_Pomiri, then Caucasian Avar=Polish=Irish=Tatar.

Regarding "looks" obviously it's unlikely that the Yamnaya resembled the average Northern European any more than EuropeMNChl people did, if genetic distance correlates simply with "looks".

(I've used Fst above as just looking at absolute f3 drift probably isn't a bit questionable method for "looks" or anything like that in my opinion, as if we take that literally, then Europeans should all look like Loschbour since a winner is him in f3 shared drift. Because he comes from a population depauperate in genetic variation and there are shared paths through other populations. Even though his population does not really contribute most ancestry. As a single summary measure Fst still leaves things to be desired (and can capture some information that isn't relevant to some questions and confuses understanding them), but in this case at least takes more genetic information in than simple sharing.)

Jijnasu said...

While there were very likely migration of Indo-Aryans into the subcontinent in the bronze age, one can't help but notice that an element of racism and euro-centrism continues to colour views on the issue. If the facts were all that mattered one would hardly stress on the 'europeanness' of yamnayans (a highly anachronistic and arbitrary term)

Davidski said...

@Anthro Survey

How does it work out that modern Swedes and Spaniards share more drift with Yamnaya than Yaghnobis and Brahmins do, respectively? Shouldn't it be pretty comparable?

No, because Yaghnobis and Brahmins have more ancestry from far away from Europe, which dampens their shared drift stats with Yamnaya. See that's my point: Yamnaya is overall, in terms of all drift paths, a package most similar to Europeans from the Northern half of Europe. So it's more than just fair to describe it as European.

@Rob

The only, arguably, 'European' component in modern Europeans is proto-WHG.

No, because EHG and CHG fused in what is now Europe to create proto-Yamnaya and eventually Yamnaya.

I'd agree with you that Yamnaya wasn't European if at least it formed outside of the modern boundaries of Europe, but that's not the case.

Davidski said...

@Jijnasu

If the facts were all that mattered one would hardly stress on the 'europeanness' of yamnayans (a highly anachronistic and arbitrary term).

Exactly. Just accept that Yamnaya is an ancient European archaeological horizon and population. No need to redefine it as something that it isn't based on semantics.

Anthro Survey said...

At this point, we should all agree to disagree because it depends on one's frame of reference.

I personally use the Bronze Age horizons of Central Europe as my reference for things because they were sort of a "TMRCA" genetic component for most modern "high-consensus" Europeans---be they Provencals or Serbs or Poles or Danes.
It is also a cultural TMRCA in many respects, too.

(Just like the late BMAC-Yaz horizon is analogous in this respect to the Iranosphere...)

What Matt said actually converges upon something else:
"as if we take that literally, then Europeans should all look like Loschbour since a winner is him in f3 shared drift"

Well, this is why I abstain from attributing most aspects of phenotype(be it craniometry to muscular fiber distribution) from limited mesolithic samples and, instead, tend focus on the formative events of the last 6000 years or so. Sein has made this point here on multiple occasions, too. Hence, another reason to take stuff like late BMAC and Unetice horizons more seriously.

Davidski said...

Matt's point about Loshbour is over the top, because Yamnaya is closer in time to modern-day Europeans than Loschbour is, and obviously it has more similar genetic structure, with about as much Basal Eurasian as modern-day Northern Europeans.

Apart from that, as I've already pointed out, just look at a map, and you'll see that the Yamnaya horizon and population came together in the part of Eurasia west of the Urals, also generally known as Europe.

So there's nothing really to debate unless some sort of agenda is being pushed at all costs.

Shaikorth said...

@Anthro Survey
I'm not sure how pseudo-haploidity of the public Yamnaya genotypes affects shared drift stats, but Kurd's processed diploid Yamnaya I0231 sample has the following IBS (genomewide similarity) ranking with modern populations:
Ukrainians=Belarusians > Pashtuns > Tatars > Estonians > Tajiks > French
The most similar populations are modern Europeans but maybe S-C Asians with high steppe ancestry are higher than we usually see.
Western Scythian is relatively similar but Tatars top the list instead of Ukrainians.
The MLBA Srubnaya is more distinctly modern European-like with Estonians > East Slavs > French > Tatars > the rest.

Anthro Survey said...

@Shaikorth

Not a huge surprise, but expect groups like Unetice, Urnfields and Lusatians to be even more distinctly European.

@Davidski

If you put it like that and look at all drift paths, then of course Yamnaya is going to share more because northern Europeans lack both the ASI-related drift and even some Iran_N-related drift(the kind specific to Neolithic S. Asians). Then there are the basal Eurasian proportions, too, that play a role and they're comparable, as you stated. Not sure if overall drift sharing with Yamnaya will still be significantly different between say, Provencals and SC Asians with minimal ASI, however. From my standpoint, it makes no difference because I take formative horizons in more recent periods to have been meaningful in establishing modern-day genetic variation(including frequencies of "trait-governing", functional alleles).

You can say I'm somewhat strict with my drift but no agenda here mate. :-) Just a matter of perspective and emphasis.

Davidski said...

Just a matter of perspective and emphasis.

Well that's what I'm doing; emphasizing for all those reading that the current consensus is that the Yamnaya horizon and peoples were located in Eastern Europe, and all opinions contradicting this aren't generally accepted.

If the consensus changes, then I'll emphasize that instead. But I don't think it'll change in our lifetimes.

Anthro Survey said...

In that case, you can go even further back in time (and west) and say that the Sredny Stog horizon was located on the banks of modern-day Dnieper. Stronger case location-wise, methinks.

It's just that back in the day, EEFs had more in common in the way of ancestry---calculator and overall drift-wise---with contemporary late neolithic Maghreb, Egypt and Syria (depending on the era) than with geographically European Sredny Stog, Novodanilovka, & early Yamna, etc. It is EEF societies like Starcevo-Kris that are often termed "Old Europe". Hybrid individuals akin to later Beakers did exist early on, but restricted to Ukraine, small in number compared to EEFs and Steppe at the time and without cultural idiosyncrasies.

Anthro Survey said...

Here is a fairly straightforward biochem analogy illustrating my perspective on things---genetics or otherwise.

1)Imagine two proteins. Same proportions and even numbers of constituent atoms(N,O,C, H & S), yet they are arranged differently, i.e diff amino acid composition and sequence, hence different 3D geometry. One is a membrane transport protein while the other is an enzyme operating under aqueous and acidic conditions.

2)Now, imagine two proteins---both enzymes---that aren't QUITE as similar(but not overly dissimilar) in raw atomic proportions. Yet, they share an important catalytic domain spanning a huge chunk of their sequence and 3D geometry. They also operate under fairly similar pH, temp and solvent conditions. Lastly, they catalyze the same reaction.

When it comes to similitude, I prioritize the shared domain in the second scenario over the overall atomic composition in the first, but, again, that's just me.

Ric Hern said...

This makes me think of that post about the Pneumonic Plague that spread from the Altai Westwards.

Maybe some Afanasevo migrated back to the Eastern Parts of Eastern Europe before the Andronova expansion. The earlier Andronova could have mixed with these people that diluted the EEF signature already....?

The earliest Andronova expansion could have been male mediated changing the Y-DNA to R1a before this group migrated Southwards from the Western Altai region ?

Spanked said...

"Europe is generally considered as separated from Asia by the watershed divides of the Ural and Caucasus Mountains, the Ural River, the Caspian and Black Seas, and the waterways of the Turkish Straits." - Wikipedia

This was the textbook definition I was taught in school, both in Canada and the UK. Geographically the Yamnaya were European.

Samuel Andrews said...

Ignoring semantics, yes, c'mon guys, Yamnaya was European. IMO, this is mostly not because of genetic affinities but geography. Defining them to modern geographically defined clusters is complicated. If you had to define them to a modern cluster it would definitly be Europe.

But I don't think we should try to fit Yamnaya into a modern clusters. Ignore modern populations. If you just look at ancient populations Yamnaya is best defined as Europe or a West Asian-European hyprid.

Yamnaya lived in Europe, its EHG and CHG ancestors mixed in Europe, half of Yamnaya's ancestry had probably been in Europe for many many millennia and had close affinities to HGs deep in Europe (EHG, then its WHG part).

I call Yamnaya European like how I call EEF Middle Eastern. EEF is most similar to modern southwest Europeans but it lived and formed in the Middle East.

@Rob,

The fact EHG's ANE ancestors may have lived in northern Asia doesn't change Yamnaya's European label. If that makes Yamnaya kinda Asian, then modern Europeans are Middle Eastern. Yamnaya had ANE ancestors in Siberia probably like 5,000+ years before its time like how Europeans had many ancestors in Turkey and the Caucasus 7,000+ years ago. Or well Inuit had ancestors in northern Asia 3,000+ years ago.

See, labeling a group to a specific geographic zone gets complicated if we define that label as having ancestors continuously living in that area for a gazzilion years. IMO, what matters is if that population formed in that region. Yamanya formed within Europe.

Shahanshah of Persia said...

@Anthro Survey Your wording was a bit confusing for me, sorry about that. I thought you were contradicting the claim, but never mind. You're right, we do not. We need much more solid evidence, to be sure. Also, I was wondering, how much BMAC admixture do you think the Indo-Aryans had before entering India and Iran? David is certain that it is not much, but I wanted to hear your opinion on the matter. Alright, thanks for that little explanation there at the end. Though, didn't the steppe invaders avoid hybridization until well into their stay in India? Hence, the caste system.


@Davidski I was wondering, are you on Anthrogenica?

@Jijnasu Realistically speaking, they were Europeans, though.

Anonymous said...

So..... My interest is the complexity of the IA migrations and what pre-IA populations in the region looked like. The ASI image is interesting, since it makes us ask what the Pre_IA northwest subcontinent may have looked like.

Shahanshah of Persia said...

@Anthro Survey Another question I wanted to ask was regarding your opinion on BMACization and its extent. Do you think that the Iranics who entered Iran were BMACized, whereas the Indo-Aryans were not? If so, is there any evidence for this? BMACization seems unlikely for South Asian populations, only because the IVC already had a decent amount of Neolithic Iranian DNA, and modern day north Indian upper caste populations (Brahmins) do not show as much as they should if there was indeed a hybridization. This brings me to another question, if the Indo-Iranians were not BMACized, then what were they? Since we have facial reconstructions of the BMAC people, they certainly were not Steppe influenced, but could it be that the Indo-Iranian formation did not have much of a genetic connection, but more-so via cultural interaction? Thank you.

Apóstolos said...

"So R1a-Z93 should appear in South Asia at the same time as Yamnaya-related ancestry from the steppe, and only become relatively common there during the final phase of the Indus Valley Civilization, or even after its collapse."

So you think that R1a-Z93 with Yamnaya-related admixture can appear (in Pakistan and NW India?) even before 1900 BC but it should become relatively common between 1900-1300 BC (Late Harappan) or later (for example up to 1000BC or what?)

I asked because I am interested on what you think is the terminus ante quem, the latest possible date the events described by AIT/AMT may have happened.

Colin Welling said...

If the facts were all that mattered one would hardly stress on the 'europeanness' of yamnayans (a highly anachronistic and arbitrary term)

There are facts and there is understanding. Facts like where, when, and shared drift are good but, without some understanding, there is no meaning.

Calling the yamnaya European is insightful because it emphasizes a few things about the broader picture. One is that WHG/EHG was all across Europe/Siberia and exclusive to it. Another insight is that Europe had most of its genetic diversity by the start of the neolithic and only reshuffling from within Europe happened after that (plus some CHG). The yamnaya were the last major reshuffle and the one closet to modern europeans.

Basically, the yamnaya were mixed europeans that ushered in modern europeans. Calling them European, even though they arent modern europeans, makes sense to me.

One time I would agree with you is if someone were to emphasize the Asianness of MA/ANE. Asia wasnt really formed same way that we understand it today.

jv said...

@ Davidski,
Changing the subject, so sorry! Just ordered an Autosomal DNA test from FTDNA. When will you be accepting autosomal DNA interpretations? ? January? February? Thanks, jv

Ric Hern said...

So it is basically the Early Andronova horizon admixing with Afanasevo/Repin relatives and thereby decreasing the EEF and increasing the Yamnaya.

So the early Andronova (Potrovka ?)spread was most likely male mediated and therefore the change from R1b to R1a without changing the Yamnaya relatedness of the previous inhabitants too much...?

Vara said...

@Davidski

Do you know the dates of this suggested route?

The South Western circle is clearly Jiroft culture, which is an EBA culture with the oldest "Indo-Iranian" elements as Sarianidi has suggested and it did affect the Late Harappan period and BMAC. If the Steppe admixture is found there then it's game over.

Davidski said...

@Shahanshah of Persia

You sort of keep asking the same thing about BMAC and South Asia, but no one can really answer your questions at least until we see the South Asian aDNA paper or even analyze the data.

@Apóstolos

Really can't add anything useful to what I've already said in regards to your question.

@jv

Hopefully January sometime.

@Vara

I don't know.

@All

Whoops, may have deleted some comments by mistake. Sorry.

Davidski said...

@All

I had to delete a stupid comment from commentator Bronze.

He was claiming that, since we're still waiting for prehistoric ancient DNA from South Asia, we can't assume that there was a migration of an ancient R1a-rich population from Eastern Europe to South Asia.

In fact, he seems to think that R1a might be native to South Asia, and thus the R1a that we're seeing in Mesolithic, Neolithic and Bronze Age Eastern European samples might be from South Asia.

I cannot allow such nonsense to be posted here. People, please, if you want to post alternative views here, then at least make an effort to come up with smart and sensible theories that are at least worth considering.

There's no hope that the R1a-M417 and R1a-Z93 that is being found in the ancient remains on the steppes got there from South Asia. Go and find a good therapist right now if you think this is still a realistic possibility. Good luck with that.

Matt said...

@Davidski, general point is only saying that considering highest shared drift by f3 (without other factors of similarity in genome wide diversity and sharing, or modeling), does not tell you which populations have most of its ancestry from an ancient, or really necessarily is that much use as a measure of distance.

@Spanked, yet, of course, Wikipedia goes on to say, in its next sentence: "Yet the non-oceanic borders of Europe—a concept dating back to classical antiquity—are arbitrary and amount to a historical and social construct." (classical antiquity a bit of WTF for any rando arbitrary modern day borders in Russia, since classical antiquity had not mapped there).

ryukendo kendow said...

The genomes from South Asia will span a period of time from what we've heard, from the Mesolithic to Neolithic and later. It will be the changes in ancestry and their synchronisation with cultural transformations and connections to outside the subcontinent that will more empirically nail down the AMT (or not). The genetic background of just the Swat valley samples alone will suffice for some, but not for the most stubborn, who would want to take a look at the populations that preceded them.

Davidski said...

@Matt

Well I did mention the major proviso that formal stats were chunky as a method for estimating genetic affinity. But at the same time they're very useful for testing for levels of European-specific drift. This is why Loschbour, and indeed all European hunter-gatherers, are such magnets in such tests.

The reason I said that your point about Loschbour was over the top, was because the WHG formal stats in this context are something of a quirk, and unlike Yamnaya, WHG is a major outlier relative to modern-day Europeans in other tests.

Rob said...

@ Sam

Yes I know, I just like to raise arguements for arguements sake sometimes

Seinundzeit said...

All,

Somewhat relevant to the question of contemporary Steppe_EMBA genetic affinities...

For what it's worth, this is what one finds, when one attempts to model Steppe_EMBA using only contemporary populations:

48.60% Tajik_Pomiri + 4.95% Kalash + 0.25% Ghilzai Pashtun
37.35% Latvian + 7.90% Udmurd
0.95% Tabasaran

"distance%=7.4638 / distance=0.074638"

Not at all identical to modern Europeans.

Rather, more like being intermediate between South Central Asians and Northern/Eastern Europeans.

Which makes sense, since Steppe_EMBA-related ancestry peaks in both Northern/Eastern Europe and South Central Asia.

So genetically, I wouldn't identify them so easily with modern European populations; they are an essential ingredient in the ethnogenesis of modern Europeans, but the same situation holds for populations in the northern Caucasus and southern Central Asia/northern South Asia, so why project contemporary genetic boundaries into a past which was foriegn to all of us?

In geographic terms though, I suppose that one does have a solid basis in calling them European.

But even then, we must admit that Europe is just a continuation of Eurasia; it's pretty far from being a geographically objective construct.

Labeling is always, in a very fundamental sense, arbitrary.

So, why spill so much ink over something so subjective? The genetic data is the most interesting aspect.

And, if one is truly/deeply interested in the question of which contemporary populations bear the closest phenotypic resemblance to Steppe_EMBA, why not just run an IBS that only involves SNPs implicated in pigmentation and cranio-facial morphology (Steppe_EMBA vs a whole slew of contemporary populations)?

That would be very far from definitive, and does involve some technical issues, but at the very least it would give us a very broad/general idea.

Anonymous said...

@Shahanshah

BMAC facial reconstructions? Where can I find them? I tried googling it, but it just gave me unrelated results.

Anonymous said...

Also, if I may note one thing: the red circles in the Iranian plateau explain the Indo-Aryan substrate in some Iranian languages, in particular the reintroduction of a word with an S-sound which had already become an H-sound in Iranian.

I would like to see how this might tie into the Mitanni. Any word of genetic studies on their elites?

Samuel Andrews said...

@Seinundzeit,
"So genetically, I wouldn't identify them so easily with modern European populations; they are an essential ingredient in the ethnogenesis of modern Europeans,"

That's the thing. Populations from 1,000s and 1,000s of years ago won't fit perfectly within a single modern cluster. Yamnaya fitting perfectly within the European cluster is not why they should be called European. They should be called European because they lived in Europe and descend to a large degree from very ancient Europeans (EHG).

Shahanshah of Persia said...

@aniasi There's only one, to this date. It's based on skulls found in Gonur Depe:

http://i45.tinypic.com/r7q6h1.jpg

Carlos Aramayo said...

To me, based partially on Anthony`s view, the escenario is that after Anatolian split there were 3 basic early migrations from Souther Russia´s Yamnaya people 1) To Poland/ Germany forming Corded Ware Culture (3000 to 2500 BC), 2) to the East, forming Afanasievo Culture in Altai near and even into China (3000 to 2500 BC), and 3) to South Asia, into Indus Civilization, arriving around 2500 BC, at the beginning of Mature Harappa phase (Davidski suggests this happened at the end of this civilization). The case is that migrations 1) and 2) were "successful" by implanting the Indo-European language and culture as well as genetical ancestry, but migration 3) ended in the assimilation of Indo-Europeans into indigenous Harappan people, leaving only genetic traces there. Centuries later, in second milennium BC, Atharvavedic first and next Rigvedic people arrived in South Asia (the same escenario as that of Parpola`s hypothesis), these ones however moved through Sintashta, Andronovo and BMAC, the Indo-Europeans arriving to Indus civilization in third millennium BC did not.

Carlos Aramayo said...


This is the link to pdf: "Crossroads: Multi-disciplinaryinvestigations of South Asia’s past" 15 December 2017, Hosted by the Department of Archaeology Max Planck Institute for the Science of Human History, Jena, Germany Organised by Ayushi Nayak


http://www.shh.mpg.de/740868/s_asia_workshop_schedule.pdf

Shahanshah of Persia said...

@Davidski You're right, but what's wrong with speculating? Sorry, I missed your reply mate. But regardless, it's good nonetheless to speculate about these things because we already have significant evidence of BMAC's linguistic influence on the formation of the Indo-Iranians. It's just a matter of time before we get the samples needed. Though, I know that you have already hypothesized that they were Chalcolithic Iranian, not Neolithic Iranian.

Seinundzeit said...

For fun, since Steppe_EMBA are construed as 50% South Central Asian and 50% Volga Uralic + Northeastern European when forced into the context of contemporary variation, I wanted to see how other ancient populations stack up.

Natufian:

84.30% BedouinB + 6.60% Yemenite_Jew + 0.10% Egyptian
7.25% Ethiopian_Amhara + 1.10% Biaka + 0.05% Ethiopian_Tigray
0.60% Papuan

distance=23.639

Levant_N:

71.15% Yemenite_Jew
26.10% Sardinian
2.45% Bedouin_B
0.20% Moroccan
0.05% Sephardic_Jew
0.05% Tunisian

distance=11.6586

Europe_EN:

90.80% Sardinian
2.30% Cypriot
0.80% Italian_South

followed by a whole slew of Southern European and Near Eastern populations.

distance=6.5256

Europe_MNChL:

85.95% Sardinian
11.25% Basque_French

followed by a whole slew of European populations.

distance=6.7402

WHG:

84.0% Latvian
13.6% Karelian
1.6% Estonian
0.5% Kosipe

(hyper-European)

distance=21.7285

Now, later steppe populations.

Steppe_MLBA:

43.60% Irish + 29.80% Lithuanian
20.95% Ghilzai Pashtun + 0.10% Tajik_Pomiri
5.50% Udmurd + 0.05% Komi

distance=4.8196

Sarmatian-Scythian:

35.2% Ghilzai Pashtun + 0.7% Tajik_Pomiri
34.0% Udmurd
29.6% Irish + 0.4% Lithuanian

distance=4.7592

So yeah, the only ancient populations that show South Central Asian signals are ones from the ancient steppe (especially Steppe_EMBA and Sarmatian-Scythians).

Interestingly, Iran_N doesn't get much of proper South Central Asian admixture; instead, just comes out completely Balochistani.

Iran_Neolithic:

84.70% Makrani
11.95% Brahui
1.60% Balochi
1.40% Biaka
0.20% Georgian
0.15% Ghilzai Pashtun

distance=11.8812

Iran_Chal are also fairly interesting:

Iran_Chal

37.95% Assyrian
32.80% Makrani
28.95% Georgian
0.20% Biaka
0.05% Iraqi_Jew
0.05% Kurdish

distance=5.8174

Davidski said...

@aniasi

Apparently there ara lots of ancient Armenian remains at the various labs being tested, but I've not heard anything about Mittani elites.

@Carlos Aramayo

I'm skeptical that there will be much, if any, steppe admixture in the Harappan samples, and if there is any, then only in the very late ones.

@Shahanshah of Persia

Yes, it's fine to speculate up to a point, but I don't have these sorts of detailed answers for South Asia yet, and won't until the relevant ancient data comes out.

Shahanshah of Persia said...

@Davidski True, true, but at the same time can you tone down the complete 100% unaltered Steppe speculating, a bit. Because, as you said, we don't have IVC South Asian samples, and therefore, we still cannot conclusively prove that they had zero BMAC influence (a truly flawed speculation). As I have said, I don't go full Nirjhar and say that they had significant BMAC admixture, as I have previously stated 10 to 30% at the most, but likely in between that figure, 15 to 25%. Also, keep in mind that the Iranians split from BMAC and went through Yaz, picking up more native admixture. Have you seen the Persian depictions from Persepolis and Susa? They look nothing like Europeans, but more-so Iranians, even their skin tone in brown. These urbanized BMACs played a crucial role in the transformation of the Proto-Indo-Iranians into the Indo-Iranians, again my opinion. Furthermore, just as the Yamnaya blended with the natives of Europe (EEF), why can't we assume that they blended into the natives of Central Asia (BMAC Neolithic Iranians)? It's only a logical conclusion, in my honest opinion.

Davidski said...

@Shahanshah of Persia

I don't know how much BMAC ancestry there is in South Asia. There might be a lot in parts of the north, but probably very little in most of India.

And considering that Iranians today have about 20% Bronze Age steppe ancestry, and obviously the Indo-Europeanization of Iran did not involve the wipe out of the Elamites and Hurrians, then I'm not at all surprised that old Iranian busts and paintings depict people who essentially look Near Eastern rather than modern-day European.

Davidski said...

@Shahanshah of Persia

And let's not get into WN politics here. I don't want this comments section to go that way.

Shahanshah of Persia said...

@Davidski Oh, alright. No worries, I understand.

Nirjhar007 said...

''No, there is no evidence of an “aryan migration” in the sense that it's historically been written about.''

Nirjhar007 said...

BTW as always, a great pleasure reading some comical stuff here....

Carlos Aramayo said...

@Nirjhar,

you quoted Dr. Nayak`s tweet:''No, there is no evidence of an “aryan migration” in the sense that it's historically been written about.''

Recent (15 December 2017) workshop "Crossroads: Multidisciplinary investigations of South Asia`s past" was organized by Ayushi Nayak. Her credentials are:

"Ayushi Nayak received her BA in Archaeology and Anthropology from the University of Oxford. Her dissertation, 'A Stable Isotope Approach to Farming Ecologies in the Indian Neolithic-Chalcolithic', was the first study to apply stable isotope methods to human, faunal, and botanical remains from prehistoric India. Ayushi is now a PhD Student at the Max Planck Institute for the Science of Human History. Her research focusses on the nature of the different trajectories of human activities in prehistory that have led to the hyper-diversity that defines the Indian sub-continent today. Through the application of biomolecular approaches, her work explores different aspects of the human past in South Asia, such as diet, early farming strategies, population movement, and inter-cultural interactions. In addition to this, Ayushi is interested in approaches to decolonising archaeological and anthropological theory, public engagement with cultural heritage, and humanist perspectives on integrating scientific method with social theory".

Currently she`s involved in the project "Biomolecular Prehistory of South Asia". This project applies a novel, multi-proxy approach, incorporating stable isotope analysis, dental calculus, proteomics and aDNA, to elucidate changes in diet, demography, and ecology across major cultural transitions in South Asia. Take a look at:

http://www.shh.mpg.de/306992/Roberts-Biomolecularprehistory

On the other hand, the workshop mentioned above had two presentations even more promising than that of Dr Vidale, these were:

Niraj Rai, "Genetic makeup of South Asian populations", and
Christina Warinner, "aDNA results from Nepal"

Shahanshah of Persia said...

@Nirjhar007 There was an Aryan invasion, just as it was written about by the British. Stop denying the realities, and stop acting like a clown. Indian civilization was begun by Vedic Aryans who arrived from the Steppes of Central Asia and transformed India. This is 100% the reality, stop being in denial.

Shahanshah of Persia said...

@Davidski Quick question, do you think these Swat Valley samples resemble the early Aryans who migrated into India? If so, they should be interesting. Will they be published soon? Also, I was wondering, when can we expect the ASI-rich Steppe-less IVC samples? Do you think that they will be heavily Iran Neolithic, heavily ASI, or in between?

Thanks, David.

Davidski said...

Yeah, the earliest Swat Valley samples should be a good proxy for the early Indo-Aryans moving into India.

I don't know whether the IVC samples are ASI-rich or not, but apparently they do have ASI.

No idea when the paper is coming. Should be soon I guess, unless some of the Indian institutions/scientists involved want a lot more samples or something.

Davidski said...


@Carlos Aramayo

On the other hand, the workshop mentioned above had two presentations even more promising than that of Dr Vidale, these were:

Niraj Rai, "Genetic makeup of South Asian populations", and
Christina Warinner, "aDNA results from Nepal"


Rai is just rehashing data from a couple of old papers. See here...

Moorjani et al. on recent population mixture in India

Warinner is talking about this...

Ancient genomes from the Himalayas

So no, not more promising than this...

Swat Valley "early Indo-Aryans" at the lab

And Ayushi Nayak can decolonise whatever she wants, including the Aryan invasion. But the ancient data will do the talking for itself, and indeed it already is.

Matt said...

@Sein, may be interesting to you, may not be. Using the Fst PCoA methods, I went back to the Eurogenes K13, which is pretty old school now and pre-adna but does have a fair amount of detail on the modern structure where more recent Eurogenes ADMIXTURE optimized for big ancient proportions (ANE, WHG, etc.) don't.

Using the component Fsts from that, I produced a Fst PCoA. I then masked out the non-"West Eurasian" componants (South_Asian, East_Asian, Siberian, Amerindian, Oceanian, Northeast_African, Sub-Saharan) for all populations with less than >85% in those (leaving just North_Atlantic, Baltic, West_Med, West_Asian, East_Med, Red_Sea).

Finally using those proportions, and the method of calculating Fst using the square of euclidean distance on the Fst PCoA dimensions, I produced a PCoA based on position using only "West Eurasian" components: https://imgur.com/a/f5cvV

Biggest counterintuitive thing for me was the old K13 West Asian component actually came out very Iran_N in this, strangely, where I would've expected it to be kind of a Caucasus like component, with the Iran_N falling instead into the South Asian component. (That is Iran_N is more like "West Asian in the flesh" than CHG is? Though they are both fairly similar). Doesn't look like that here.

I thought this might be interesting because certainly signs of layers of S Asian ancestry here, with clear clines in the S Asian populations even after removing the S Asian component (compare the positions of the non-S Asian parts of Brahmin UP, Pathan and Sindhi for ex, or for Kol Scheduled Caste from Uttar Pradesh, Chamar from Punjab and Sakili). South Asian component, which hits from 25% in Afghan Pashtun to 40% Pathan to 77% in Chamar, looked like a mixed West Eurasian+East Eurasian component, but it seems like here this is apparently independent of a cline in Iran_N like ancestry in this data...

Makes me very interested to see what we'll find in India; will there be a layer of Iran_N like ancestry in India which is much more ancient than a more recent wave that actually entered with the Neolithic. Then, more differences between Neolithic and Bronze Age ancestry in Indo-Aryan / North Indian groups and Dravidian / South Indian than we'd expect from a single Neolithic wave of Iran_N-like?

(If you're looking at the graphics, another thing you can contrast the neighbour joining based on component Fsts with the kind of neighbour joining from real Fsts, which is far more granular and bumpy, reflecting the much more rich kind of variance in real populations compared to what can be captured with even 13 components, albeit that I've reduced these by taking out the non-West Eurasian components.).

Shahanshah of Persia said...

@Davidski Alright, I am looking forward to the Swat samples. Do you think that we will get an update on samples from BMAC in the coming year, as well, or no? I am certain that we may, though, it can take a while.

Oh okay, yeah it makes sense, though I doubt they have more than 30% ASI.

Yeah, but it sucks since people like Nirjhar are overtly proud about their supposed native origins that they do not want to acknowledge the facts. More samples are not going to change the reality my friend, we all know this very well, lol.

Davidski said...

@Shahanshah of Persia

The BMAC samples are likely to be in the same paper as the Harappan and Swat samples, and this paper should be out next year, but who knows really, since it's such a controversial topic.

It might take a while for some of the involved parties to decolonise the data to their satisfaction. LOL

Shahanshah of Persia said...

@Davidski Lol, exactly! Anyway, I hope they release them soon, lol.

Carlos Aramayo said...

@Davidski,

you wrote Niraj Rai presentation "Genetic makeup of South Asian populations" is
"just rehashing data from a couple of old papers.

I do not think Max Planck Institute held a workshop with only rehashing material.

Did you attend the workshop at Jena?

Of course that the aDNA samples should talk for themselves. Anyway, South Asian aDNA will be published by Niraj Rai`s team. But I feel you`re adding unnecessary controversy.

Davidski said...

@Carlos Aramayo

I do not think Max Planck Institute held a workshop with only rehashing material.

That's exactly what they did.

Feel free to get in touch with Ayushi Nayak and ask her if any new data were presented by Rai. She'll tell you no, and that it was a review of the current state of knowledge, essentially based on two Harvard-led papers that came out in 2009 and 2013.

Practically the only genuinely new thing there was that map by Vidale.

Did you attend the workshop at Jena?

No, but I've got a lot of insight into this area of research, and then some.

Anyway, South Asian aDNA will be published by Niraj Rai`s team.

Not really. I won't get into the details here, but most of the South Asian aDNA data are being generated by Harvard and Max Planck.

But I feel you`re adding unnecessary controversy.

Controversy yes, unnecessary no.

Shahanshah of Persia said...

@Davidski How did they get it? Wouldn't they need permission from the Indian authorities to extract it? The good news is though that we are finally getting these samples, and I am quite excited. This should be the nail in the coffin of the OIT. Let's hope they get the results released in the first quarter of 2018. On a side note, I wanted to ask you another question, though, not repetitive I hope.

Is it safe to say that the Median/Achaemenid elite were genetically European early on, or do we not have much information on this for the time being? Also, will the SWAT samples be representative of the Indo-Aryan elite which emerged during the Vedic period?

Thank you, I would appreciate some feedback from you.

Davidski said...

@Shahanshah of Persia

How did they get it? Wouldn't they need permission from the Indian authorities to extract it?

I don't know what the procedures were for exporting and testing the ancient samples. I read somewhere that they were going to use a lab in India, but I don't think they did in the end.

I am concerned that the paper will be seriously delayed for one reason or another as it becomes obvious to even the most stubborn OIT proponents on the team that OIT is a dud, but I don't think it'll be scuttled, because that would be very controversial.

Is it safe to say that the Median/Achaemenid elite were genetically European early on, or do we not have much information on this for the time being? Also, will the SWAT samples be representative of the Indo-Aryan elite which emerged during the Vedic period?

No idea. I need to see some ancient data to have any sort of opinion on details like these.

Carlos Aramayo said...

@Davidski,

You just keep writing things like: "I've got a lot of insight into this..." but "I won`t get into details..."

And you ask me to ask Ayushi Nayak, from Max Planck institute, the same person you just laughed at in a previous message. And next, in order to dismiss Niraj`s work you try to call my attention that Max Planck is actually the institution which generated the aDNA data in which you trust. Are you joking?

Shahanshah of Persia said...

@Davidski I definitely agree with you, 100%. I think that the Indian authorities have been working hard to cover this up, as for them it would be a great disgrace to know that their culture and civilization originated outside of India, in the Steppes of Europe. I guess we have to just wait it out. But hopefully the results are released earlier this year.

Alright, to your second point. I guess we just have to wait, but the upcoming results should at least provide us with some clues in regards to the peoples of the IVC, and the Aryan elite who conquered them.

Shahanshah of Persia said...

@Carlos Aramayo Indians try to play things off. But the truth is that Indic civilization originated on the Steppes. Take it or leave it, but it's the truth.

Davidski said...

@Carlos Aramayo

And you ask me to ask Ayushi Nayak, from Max Planck institute, the same person you just laughed at in a previous message. And next, in order to dismiss Niraj`s work you try to call my attention that Max Planck is actually the institution which generated the aDNA data in which you trust. Are you joking?

Well, seriously, who in their right mind sets out to "decolonise" theories before even seeing all the scientific data? What if in the end all of the data clearly show a colonization of South Asia during the Bronze Age? What is she going to do then?

I guess she missed her calling. She should've been born around 200 years ago to lead a rebellion in some poor colonized land.

But you can still ask her whether Rai was rehashing old stuff. I can assure you that he was, and since she organized the conference, then she'll be able to confirm that for you. So ask her.

And I do trust the accuracy of the aDNA data coming out of the Max Planck Institute for the Science of Human History, but that's more because of the fact that they're working with Broad MIT/Harvard, than any respect for the said institute.

Actually, to be brutally honest, I don't have a high opinion of the said institute. Why? See here...

Paul Heggarty: desperate or clueless?

Dead cat bounce

But hey, that's just me, and what the hell do I really know anyway? Keep in mind though, that the proof of the pudding is in the eating. So come back here in a year or so and then we'll chat about who knew what they were talking about.

Carlos Aramayo said...

@Shahansha,

I m also aware that data tend to point out that Yamnaya people are ancestors or even the same people who moved from Pontic Steppes, after 3000 BC, towards South Asia. Please read my previous messages. But I do not feel "academically confortable" in scenarios where we suggest "conspiration theories".

Shahanshah of Persia said...

@Davidski To be fair, I think I know why Indians are quite hostile to the notion of an Indian invasion. Because, let's be honest here, while the Aryans did invade India and dominate during the Vedic era, they were not the highlight of Indian civilization, though it was indeed derived from them. The peak of Indian civilization was during the Gupta period, which is often referred to as the classical period in Indian history. The Gupta dynasty were not even of a high caste origin. The Mauryan period was not far behind either. Not to mention all of the other South Indian dynasties. Also, Medieval India had quite a history, and many cultural and scientific achievements in India came far after the original Aryan invasion, at which point it's safe to say that there were not pure Aryans left. So, what's happening here is that Indians feel that if they cede a European origin for the Vedic Aryans, then it would mean that their entire civilization was European derived, and hence, the Raj was justified. Now, many Indians do not want to admit this, and hence, they become vehemently anti-Aryan migration. The truth is that Indian/Indic civilization was ultimately a product of India more than anything, with an early boost from the Steppe peoples who conquered the declining Indus Valley Civilization. We actually see a similar pattern throughout Indian history. In fact, we see an influx of Steppe peoples into India immediately following the collapse of the Guptas, never mind the Greek rule prior to that. The Kushans, Hepthalites, etc., all marched into India and continuously established kingdoms in the northwest. Even during the medieval period we see Turks and Turco-Mongols invading and establishing kingdoms. I think all of this is a hard pill to swallow for the most staunch Indian nationalist. All of these steppe people gave a boost to Indic culture, but were ultimately sucked into it. Any thoughts, David?

Shahanshah of Persia said...

@Davidski First sentence, Aryan invasion not Indian invasion, sorry about that, I should've proofread.

@Carlos Aramayo Oh, true. By the way, I am not bringing up any conspiracy theories here. And Davidski is right to assume that the Indians do not want the truth to leak.

Matt said...

@Sein, attempt to use a regression to place the South Asian component from Eurogenes K13 onto a PCoA+Fst - https://pastebin.com/xD8nq0Hz (see bottom two rows).

Some simple example fits: https://pastebin.com/3F3Eu4p4

A few more complex example fits: https://pastebin.com/PGhBFLLv

(A bit more on the the complex fits: They don't have basically different patterns, but do show a marked preference for Armenia_MLBA, then if that's not available Iran_CHL, then if that's not available Steppe_MLBA.

To me, in this data at least, it seems in contrast to assumptions and some formal models, a slight offset of Western farmer ancestry, preferably Levantine but EEF if that's not available, actually does seem to improve fits in South Central Asia. So as well as the IE expansions, South Central Asia may have been drawn into the Near Eastern interaction sphere, rather than purely going its own way after the Zagros Neolithic.

(Perhaps this is analogous to how East Africa looked to have neolithic expansion ancestry which was purely Levant Neolithic related at first blush, and predominantly is... but then Skoglund's recent examination of African ancient dna found some signal of Iran Neolithic, which appears to have come in with Arabic speakers, linked with Gulf Arabs who would logically given their location have Iran Neolithic related ancestry).)

Davidski said...

@ Shahanshah of Persia

I definitely agree with you, 100%. I think that the Indian authorities have been working hard to cover this up, as for them it would be a great disgrace to know that their culture and civilization originated outside of India, in the Steppes of Europe.

I didn't say that exactly.

This isn't a problem across the board in India, only in certain circles. Many Indian academics have never considered OIT as anything but lunacy. See here...

https://thewire.in/60116/the-chauvinism-in-indian-archaeology-is-very-evident-shereen-ratnagar/

Davidski said...

And here...

https://www.harappa.com/video/remote-past-recent-past

Shahanshah of Persia said...

@Davidski Thanks, I should've clarified that it's mainly BJP influenced/related circles who are opposed to the AMT. Thanks for sharing these, appreciate it.

Shahanshah of Persia said...

@Davidski I wanted to ask you, will you have tests based around the SWAT valley samples when they're released? Thanks.

Seinundzeit said...

Matt,

"Makes me very interested to see what we'll find in India; will there be a layer of Iran_N like ancestry in India which is much more ancient than a more recent wave that actually entered with the Neolithic. Then, more differences between Neolithic and Bronze Age ancestry in Indo-Aryan / North Indian groups and Dravidian / South Indian than we'd expect from a single Neolithic wave of Iran_N-like?"

Interesting thoughts. And, based on some info I've heard concerning upcoming aDNA, very sensible thoughts.

In my estimation (and for what it's worth), there is a very ancient layer of South Central Asian ancestry that extends rather deep into peninsular South Asia (basically, very similar to Iran_Hotu, but with even more of the ANE-related ancestry that's at play with Mesolithic/Neolithic Iranian plateau populations).

With that being said, this stream of ancestry seems to have been totally replaced in southern Central Asia (so, only a noticeable factor in southern India).

In addition, there is the far more widespread layer of Iran_N ancestry across South Asia, but peaking outside of the sub-continent in peripheral West Asia (Balochistan and Hormozgan).

Finally, there is Iran_Chl-related ancestry, but with a stronger CHG-related affinity than the currently sampled Iran_Chl. This is the primary Near Eastern component in southern Central Asia, whether we are talking about Pashtuns, or Tajiks, or Pamiris, or the smaller Pashtunized Eastern Iranian populations in the Pak-Afghan highlands (Urmur, Baraki, Waneci, etc).

Although, the Dardic and Nuristani peoples do have a combination of both Iran_N and Iran_Chl (as do the northeastern Gharghakht Pashtuns, since they have heavy amounts of Dardic/Nuristani admixture).

Regardless, I've found that the ENA reference plays a very large role in determining the sort of "western" shift seen with the Near Eastern ancestry.

For example, with my own ASI simulation I really can't find any Armenia_MLBA in South Central Asia, only Iran_Chl, while only Iran_N dominates South Asia (just like the pattern in eigenvector scaled Global_10).

For a couple of reasons, I think this will turn out to be correct.

But, until we see aDNA from Tajikistan/Turkmenistan/Afghanistan/Pakistan/India, the details will be rather fuzzy/unclear.

postneo said...

yes David invented red circles. Others have adopted the idea from him.

Davidski said...

@Shahanshah of Persia

I wanted to ask you, will you have tests based around the SWAT valley samples when they're released? Thanks.

Sure, if they have enough data.

@postneo

yes David invented red circles. Others have adopted the idea from him.

You're wrong, as usual. They're ellipses.

Salden said...

>yes David invented red circles. Others have adopted the idea from him.

Did Europe get invaded by Indians?

Shahanshah of Persia said...

@Sein Any behind the scenes information on BMAC and SWAT?

@David Thanks, and theoretically speaking, if you had to predict the genetic composition of Harappa and BMAC samples what do you think they would most likely be (only hypothetical here, since you obviously have a better understanding and foresight than most of us here)?

Here's what I think:

Harappa:

25 to 50% ASI
50 to 75% Iran Neolithic

BMAC:

60 to 80% Iran Chalcolithic
20 to 40% Iran Neolithic

Any thoughts on my predictions?

Matt said...

@Sein, yeah certainly v. true re: placing the ENA reference having an impact changing the structure of the non-ENA part. Note that (to bang on again) the simulation of the Eurogenes K13 South Asian component is not really an ENA reference, as well! The above is more of a method that goes:

"Assume Eurogenes K13 is right about the existence of a South Asian component in roughly those proportions, and that the South Asian components generally generated by ADMIXTURE are roughly correct; after that is accounted for, how is the other ancestry in South Asian groups best modeled in the ancient dna, and what structure does it show?".

And then it still does show extensive structure in Iran_N vs Steppe_EMBA in expected ways, which it at least confirms that the variance is independent of whether that ADMIXTURE component is present or not (e.g. South Asian component in Eurogenes K13 is not "gobbling up" all of either Iran_N / Steppe_EMBA in disproportionate ways; doesn't seem to necessarily be just some rolling together of Iran_N / Steppe_EMBA with ASI because we lacked proper ancient references).

The alternative is something like Reich's method, which instead takes the (not unreasonable) working assumption that ASI should be part of the ENA clade, then attempts to use best proxies for an ENA clade member admixing into SCA (Onge / Dai) and once that is accounted for, models remaining ancestry, which is presumed to be post-Holocene ANI.

The qpAdm / f4 ratio / qpGraph are all pretty much variations on this theme using f4 statistics.

Ultimately at this level of detail there is still a bit of guesswork involved; we'll see how much Reich's working assumption holds up, or how much ADMIXTURE's stubborn finding of South Asian component in unsupervised ADMIXTURE runs is just an artefact of the method vs real best fitting.

Here's a copy of the Fst matrix David uploaded on 04/08/2017 with a few simulated Eurogenes K13 South Asian component and "Reich ASI" simulations added on at the end: https://pastebin.com/Nkge6f6A. So you can run PCoA, etc. on this yourself if you're more curious about how these "zombies" behave.

Few basic graphics for those: https://imgur.com/a/Qlx6g

Seinundzeit said...

Matt,

"Assume Eurogenes K13 is right about the existence of a South Asian component in roughly those proportions, and that the South Asian components generally generated by ADMIXTURE are roughly correct; after that is accounted for, how is the other ancestry in South Asian groups best modeled in the ancient dna, and what structure does it show?".

Yeah, I wasn't really addressing what you did with the Eurogenes K13; just making a general point.

For what it's worth, unsupervised ADMIXTURE, when hit with either a massive amount of South Asians/West Asians/Central Asians or with very few of them (quite odd, but works both ways), can produce Ks that lack a stabilized South Asian component.

For example, Zack Ajmal's K11 comes to mind; it was an unsupervised run, but instead of a South Asian component, it had a West Eurasian component strongly tied to South Asia and South Central Asia, but with a decent presence in Iran (almost identical in modality to Iran_N; but this was a few years before the aDNA revolution, so many of the commentators didn't know what to make of it, including Zack), and an "Onge" component that was around 1%-3% in Iran, 5%-10% in South Central Asia, and peaked at 65% among the Paniya.

That being said, I do completely agree with you; Indian aDNA is going to provide great insight.

Davidski said...

@Shahanshah of Persia

Harappans: depending on the sites and individuals sampled, anywhere from almost fully Iran_N to Panyia-like.

BMAC: depending on the sites and individuals sampled, anywhere from almost fully Iran_ChL to mostly Iran_N.

Carlos Aramayo said...

This is a previous (June 2016) newspaper article on Barikot excavations by Luca Olivieri's team, of course not another rehash (as Davidsky tried to suggest). Excavations report was presented at

Crossroads: Multi-disciplinary
investigations of South Asia’s past
15 December 2017
Hosted by the Department of Archaeology
Max Planck Institute for the Science of Human History, Jena,
Germany
Organised by Ayushi Nayak

https://www.dawn.com/news/1267322

"...(Olivieri) said that during the excavations the archaeologists also discovered that all the pre-Greek layers were artificially destroyed and obliterated along the Defensive Wall at the time of its construction, to make space to the fortification, revealing conspicuous traces of the Iron Age village (7th BCE). Dr Luca said that his team was currently excavating one hectare with a stratigraphy from 7th BCE to 3rd CE in Bazira. The area corresponded to circa 1/12 of the entire city. “The KP government is about to acquire all the excavated areas and a large buffer area around them. We are really grateful to the efforts of the provincial department of archaeology and the government,” he said...

Davidski said...

@Carlos Aramayo

Rai's talk was a review, based mostly on Moorjani's paper from 2013, and not on any ancient data from South Asia. Deal with it.

Carlos Aramayo said...

@Davidski,

O.K., I believe you regarding Rai`s presentation, then it`s almost obvious that Rai did not expose all the details of aDNA for Rakhigarhi and South Asia in general. I wanted to highlight that not all presentations were rehashes, as you said that "only" Vidale`s presentation was not one of them, and I was able to read some possitive comments on the Max Planck`s workshop elsewhere in the web.

Shahanshah of Persia said...

@Davidski Thanks! Recently, you wrote that you expected the SWAT valley samples to be greater than 50% Steppe EMBA, though you didn't really clarify what you meant by this. You said that they would be sort of like the Kalash, does this mean that you expect them to have some Neolithic/Chalcolithic "Iranian" admixture? Or, were you suggesting that they might have been closer to Steppe MLBA? In any event, do you think we'll find any non-Steppe admixture in the samples, and what do you think the source for this non-Steppe admixture be? I would like to see what you've speculated about this.

Matt said...

@Sein, interesting, I only really knew of the main Harappa project spreadsheet component
(https://docs.google.com/spreadsheets/d/1l87nGSIYTP-h7m-VKjB-BZcuEoWdz765nU4f_krOdd4/edit#gid=0), which is mostly more like Eurogenes K13, though does seems more ENA rich (so a bit more like pure ENA Reich ASI). Possibly from some other aspects of the South Asian component in K13 bleeding into other components.

You're right that as with all ADMIXTURE does depend on the run under consideration...

Thought these graphics might be interesting as well since it came up while I was running a regression on the Harappa component: https://imgur.com/a/G5zF5

The part of the graphs here where Harappa S Indian component was compared to Coordinate 4 were pretty interesting to me (https://i.imgur.com/ZfcfJU7.png). I'm sure it's well known to you already but seems like it shows clearly the two ANI clines in South Asia, both pointing towards Paniya from different directions.

One points from Makrani, Brahui, Baloch (low S Indian), through a gap, then picks up through Velamas, Piramali, Chenchu, Sakilli, Hakkipikki (high S Indian); the other goes from Kalash and Pashtun (Pakistan) through Kshatriya, through Dharkar/Kanjar (roughly same S Indian as Velamas), through Kol (roughly same S Indian as Piramalai), thenn Chamar (roughly same S Indian as Sakilli).

So yeah, certainly some kind of independence of the IranN:Steppe ratio from the overall S Indian cline. It looks like it's possible to have populations with a similar ANI to have different levels of true ASI. S Indian component in Harappa correlates very well with the ENA dimension, so its capturing the ENA level to a pretty high extent, and maybe probably some small portion of extra West Eurasian related ancestry.

Main gap in the cline seems to be that the Middle-High caste Indian range of S Indian is lacking members from the Balochi->Hakkipikki cline that have equivalent S Indian to Kshatriya / Brahmin UP. I wonder if this is sampling *or* people in that range just don't exist in S Asia.

Davidski said...

@Shahanshah of Persia

I expect that that Swat samples, at least the early ones, will be modeled like Kalash in Lazaridis et al. 2016, except with more Steppe_EMBA admixture.

If so, then they would have local South Central Asian admixture, both Neolithic and East/South Asian, from preceding local populations like Fergana.

But these sorts of speculations aren't very interesting anymore. I'm just waiting to see the data now.

Shahanshah of Persia said...

@Davidski Alright, thanks mate. Much appreciated! Best wishes. I do hope that they release them sooner as opposed to later. I would agree with your assessment here.

Kurd said...

@ Shaikorth

I'm not sure how pseudo-haploidity of the public Yamnaya genotypes affects shared drift stats, but Kurd's processed diploid Yamnaya I0231 sample has the following IBS (genomewide similarity) ranking with modern populations:
Ukrainians=Belarusians > Pashtuns > Tatars > Estonians > Tajiks > French
The most similar populations are modern Europeans but maybe S-C Asians with high steppe ancestry are higher than we usually see.
Western Scythian is relatively similar but Tatars top the list instead of Ukrainians.
The MLBA Srubnaya is more distinctly modern European-like with Estonians > East Slavs > French > Tatars > the rest.





The inaccuracy in the published pseudo-haploid aDNA will manifest itself to varying degrees depending on the tool/method used to calculate shared drift. The will fare worst with methods where an accurate diploid allele assessment is paramount, such as with IBD/IBS, because the pseudo-haploid will be incorrect at ALL the diploid positions in the genome, which translates to about 30% of the genome, where genome is defined by polymorphic sites only such as in your typical public dataset.

You can get an idea by looking at fig 11 and 12 on my website http://www.eurasiandna.com/2017/10/02/diploid-genotyping-low-medium-coverage-ancient-dna/ which are for Scythian I0247 which I diploid genotyped using a pipeline suited for aDNA, and which produces less reference biased genotypes (preceding figs and tables)than GATK. BTW, the numbers don't reflect the approximately 8% modern CEU contamination for that particular sample, which when adjusted for using PMDS (Skoglund) produced a slightly more E Eurasian genotype for the sample

Other methods of calculation such as ADMIXTURE are also affected to a lesser degree because an incorrect 0/0 or 1/1 assignment in a hetrozygous position in the pseudo haploid will yield a different allele frequency when compared to the true diploid genotype of 0/1 in the sample.

This said, I am testing some software that I wrote that takes IBS to the next level, because IBS doesn't tell us how much of the sharing between Pop A and Pop B is due to shared origins in the phylogenetic tree vs direct geneflow from Pop A to Pop B.

I'll have an article with results up on my website soon. Basically the test looks at all shared positions between Pop A and B with the ALTERNATE/MINOR allele to the exclusion of multiple outgroups. The runs look promising and in many cases tell a slightly different story than IBS. For example, the Yamna I0231 Samara sequence that I diploid genotyped (decent avg read depth) using the above shares slightly more drift with Caucasians and Kurds than with most Europeans, but I will emphasize that the simplistic view that almost everyone here and elsewhere take, where they rank populations according to shared drift is ABSOLUTELY useless, where they for ex say Pashtuns share more (or less) drift with a certain pop than Lithuanians. In the real world individuals from most populations overlap each other in terms of shared drift. For example, if you make a sorted table of shared drift with Yamna using individuals and not pops from various groups, you'll see that individuals from all ethnic groups are all over the place and not grouped together as most people believe.

With the Volga Scythian diploid sample that I diploid genotyped and using the above test that I devised Kurds clearly topped the list followed by various Caucasians, although I did not have other Iranics in the run. Pashtuns and E Europeans were further down, however I only had Estonians and Poles from E Europe in the run (disclaimer: none of the E Europeans from further S or E were included)

Shahanshah of Persia said...

@Davidski Speaking of naysayers, I actually wanted to share this with you: https://www.youtube.com/watch?v=qPaCUJsZyPU&t=

This is how Indian "scientists" try to debate the Aryan Invasion Theory. This has to be one of the worst arguments against it, ever! He basically rambles on about how when humans left Africa they arrived in India first and developed speech, therefore, all languages come from India and the Aryans did not invade India. This is very sad and unfortunate, the extent to which some of these people are in denial.

Kurd Dgk said...

With regards to my previous post, many will be left thinking what causes the majority of Estonians to show more shared drift with Yamna than the majority of Caucasians and Kurds using more crude methods of analysis.

I believe it is the large number of (EHG+CHG) alleles in Estonians and other Europeans for that matter which were received via other groups, and since Yamna is CHG+EHG, those alleles are present within Yamna as well, however, when those are backed out of Yamna and the test pops, the shared drift pendulum swings more towards Caucasians and Kurds.

Davidski said...

@Kurd

I believe it is the large number of (EHG+CHG) alleles in Estonians and other Europeans for that matter which were received via other groups.

Well, when you say "other groups" I hope you mean Corded Ware and derived R1a-Z645 groups like Trzciniec (Baltic_BA from Mittnik et al.), because your tests showing that N/E Europeans got most of our steppe ancestry from Karasuk look way off.

Doesn't gel with the facts at all.

The genetic history of Northern Europe (or rather the South Baltic)

Shahanshah of Persia said...

@Davidski Yeah, Karasuk completely changes the picture. Though, why do you think this might be?

Davidski said...

@Shahanshah of Persia

Yeah, Karasuk completely changes the picture. Though, why do you think this might be?

Karasuk doesn't change the picture. Balto-Slavs get their steppe ancestry from Corded Ware via Trzciniec, a Kurgan group derived from Corded Ware.

Not only the high shared drift between Balto-Slavs and Trzciniec shows this, but also the uniparental markers. Karasuk is not even in the ballpark, because it has the wrong uniparental markers.

Kurd's tests are wrong. He needs to fix them or pull them from the web. Nothing more to discuss.

Shahanshah of Persia said...

@Davidski No, I meant why does Karasuk show up as Steppe in Kurd's calculators, i.e. why does it change the picture in that particular calculator? I know that Northern/Eastern Europeans have much more steppe than South Asians and Iranians.

I know they are flawed, you have made this clear to me before. I was just wondering why the disparity between yours and his. Thanks for clarifying it for me.

Davidski said...

@Shahanshah of Persia

Clearly, there's a serious methodological flaw with Kurd's algorithm and/or data, since it fails such a basic sanity test like the origin of steppe ancestry in Eastern Europeans.

When creating tests, you have to ask the question whether the results make sense at the most basic level. And if, say, most of the steppe ancestry in modern-day Eastern Europeans looks like it comes from the Karasuk people of the Altai, who show very foreign/exotic mixture proportions and uniparental markers to Eastern Europeans, then it's back to the drawing board.

Kurd Dgk said...

@ Davidski

Well, when you say "other groups" I hope you mean Corded Ware and derived R1a-Z645 groups like Trzciniec (Baltic_BA from Mittnik et al.), because your tests showing that N/E Europeans got most of our steppe ancestry from Karasuk look way off.


Well, there is no burden of proof that I enumerate the various groups that contributed EHG and CHG to Europeans for the test to be valid. Obviously, Corded Ware would be amongst those and there maybe others yet to be discovered.

The principles behind the test are not rocket science, simply back out any minor/alternate alleles shared by European tester, Yamna, and outgroups ( for ex Yoruba, Ust, EEF, EHG, CHG, Goyet116, Papuans, Onge) because those could have been acquired by the tester via other means (other than Yamna). What you will be left with is minor/alternate alleles shared by the tester (European, Caucasian, etc) and Yamna to the exclusion of the outgroups (ie more Yamna specific shared drift).

I am not sure what Karasuk has to do with any of this. Out of curiosity where on my website have I stated that NE Europeans get most of their steppe ancestry from Karasuk because that would frankly not make any sense

Shahanshah of Persia said...

@Davidski Thanks for clarifying mate. How accurate are your tests, in your opinion? Are they very accurate? It's interesting to see that we find a lot of Steppe admixture in S/C Asia. It's incredible. These Aryans must've have been very populous for the time. The manner in which they managed to reshape South Asia was truly incredible, unlike ever before! Even Europe, they pretty much replaced 70% of the natives in the north, and 30% in the South. Truly amazing!

Are these estimations for Northwest South Asians correct?:

Pathans: 44% Steppe
Jatts: 42% Steppe
Brahmins: 40% Steppe
Gujjars/Arains/Rajputs: 36 to 38% Steppe

Thanks bro, best wishes. Keep up the excellent research.

Seinundzeit said...

Matt,

"... which is mostly more like Eurogenes K13, though does seems more ENA rich (so a bit more like pure ENA Reich ASI)."

Definitely; in fact, the HarappaWorld "South_Indian" component seems to be an almost even mix of West Eurasian-related and ENA, while the Eurogenes K13 component seems to be mostly West Eurasian (that being said, components in ADMIXTURE don't necessarily "mean" the same thing for the populations in which they appear).

To further digress on this, Everest ran the "South_Indian" component through a supervised ADMIXTURE run where the references were simply the other HarappaWorld components.

In that context, "South_Indian" came out to be 50% Caucasus, 40% SE_Asian, and 10% Papuan.

"The part of the graphs here where Harappa S Indian component was compared to Coordinate 4 were pretty interesting to me (https://i.imgur.com/ZfcfJU7.png). I'm sure it's well known to you already but seems like it shows clearly the two ANI clines in South Asia..."

Very true, especially in the context of PCA and ADMIXTURE.

Davidski said...

@Kurd

We're referring to the results from one or more of your tests that people were posting at AG. Northern Europeans, Eastern and Western, were showing unusually low steppe ancestry proportions, with Karasuk as one of the main sources of their steppe ancestry.

In theory, the method you describe might seem very simple and sound, but if in practice it produces such results, then there's a problem somewhere.

@Shahanshah of Persia

My estimates are accurate enough for now; showing around 50% steppe in the Pamirs and Hindu Kush, which falls to almost nothing in South India, although some low caste groups in North/Central India, like the Chamars, also show low steppe ancestry proportions.

I don't have time now to discuss this in any more detail, and in any case, I can't add anything more until I see the ancient DNA data from South Asia.

Shahanshah of Persia said...

@Davidski Alright, best wishes David. Thanks for clarifying.

Kurd said...

@ Davidski

I thought I was loosing my mind so I checked the spreadsheet that was put together and uploaded by one of the K12 calculator users. I sorted the results by W Steppe (And/Srub-Yam/Polt) (sheet 2 titled Steppe Only) https://drive.google.com/file/d/1Ujl4O3V_BbRyU2Qox-pTBDJQzNXIOp4m/view?usp=sharing

It seems that someone may have been feeding you false info.

As you can see Europeans scored much higher W Steppe than E Steppe (mostly E Karasuk diploids by Martiniano). In fact, E/N Europeans scored anywhere from 26-40% total Steppe, with the average around 34%, which is not very different from Lazaridis total steppe where they modeled Europeans as EEF+WHG+Steppe, which is not bad for an ADMIXTURE based calculator considering that it is not the most accurate tool out there, and considering that it is not informative to direction of geneflow.

Highest scorers of E Steppe (mostly E Karasuk) were SC and some S Asians, which is reasonable since modern lineages with the highest E Karasuk are practically in their backyard.

I would appreciate it that you yourself verify what people tell you in the future about any of my products before running off with what they say. After all I would extend you the same courtesy.

Shahanshah of Persia said...

@Kurd Dude, I remember some Pakistani dude scoring 29% Scythian on that! Your tests have some serious issues if they hint that there are people alive today who are 1/3rd Scythian. This is a serious issue, mate.

Kurd said...

@ S of Persia

You really need to get your facts straight before spreading lies like this Mr Phd in Genetics and Bioinformatics.

The Scythian samples were only 2/7 of the Karasuk-Scythian component. The component description at GenePlaza clearly states "this cluster is based on ancient genomes from the Karasuk culture supplemented with 2 IA Scythian samples. The % should be interpreted as a diffusion of DNA from the E Eurasian Steppe populations post BA, via Turkic expansions, as well as more subtle diffusion via NE Caucasus pops". I have also mentioned that myself numerous times at AG, but apparently folks like yourself like to do a disservice to everyone by spreading lies for whatever weird reason.

I will also add that since the Karasuk can be thought of as Okunevo plus a dose of Siberian Uralics/Finno-Ugrics can also share drift with them.

BTW, how is that any different than someone being modeled as 40% or 50% Yamnaya or whatever.

MomOfZoha said...

"And considering that Iranians today have about 20% Bronze Age steppe ancestry, and obviously the Indo-Europeanization of Iran did not involve the wipe out of the Elamites and Hurrians, then I'm not at all surprised that old Iranian busts and paintings depict people who essentially look Near Eastern rather than modern-day European."

Old Iranian busts and paintings reflect not only the phenotypes of the peoples of the time but also the aesthetic ideals of that culture, just like busts and paintings of any culture do. One can also see some changes in the miniature styles during the Seljuk era. But, even much prior to that time and up to the present moment certain features are emphasized in Iranian poetry and art. This is maybe best expressed in Ferdowsi's Shahnameh, in the description of Rudabeh, Zal's beloved wife, mother of the hero Rustam.

In contrast to the black haired, dark eyed, strikingly eyebrowed Rudabeh, the albinism of Zal of pale-hair is presented as a factor contributing to his parents' fear and rejection of him. Rudabeh might very well have been of Near Eastern descent, at least mythically. But, her black haired features are the very same features of countless other heroines praised by Persian poets and artists of old.

It is not safe to assume that all "Indo-European speaking" cultures would have had the same beauty ideals as Europeans, even when they had sufficiently many people with typically European phenotypes to idealize if they so preferred.

Anyway...

On a totally different note: I also want to thank you, Anthro Survey, for your insightful comments. The more I read about Yamnaya, the more I am amazed that they are considered the proxy for the "European" influence on anything east of the present European borders. There is so much to say in that regard (including the meaninglessness of present day borders, especially when it comes to the greater Caucasus region)-- much of which you already clarified -- it seems futile to say more. The passage of time (more samples and more nuanced admixture models) will hopefully clarify things itself, especially after the "Near Eastern" contribution to the Yamnaya is better understood... By the way, I enjoy reading your comments in other posts as well. Best regards and Happy Holidays.

Anthro Survey said...

@Shahanshah

I strongly agree with your hunch concerning Indo-Aryan migrants not having a whole lot of BMAC admixture in them(esp regarding calculators and North Indians getting less Iran_N than might be expected) as well as with your ASI/Iran_Chl/Iran_N proportion speculation in general. These Aryans were a highly mobile people with horses and chariots, so even a completely saltatory migration need not be automatically excluded if we were to ignore all other data.

To digress a bit---you ever looked into Seljuk Turkic expansions? Though an imperfect historical analogy, these were almost textbook saltatory migrations of horsemen: one wave moved into western Iran while the other went straight into Anatolia almost simultaneously with minimal-to-no mixing along the way. Similar 13th century migrations of Muslim Turkic refugees into Anatolia spanning hundreds of miles in a short period of time are also well-documented.

Yet, it's unlikely to have been ~zero either. Again, if David Anthony's theorizing about BMAC words and the deity Indra are correct, there would have to have been at least a bit of mixing to occur to ensure extensive cultural hybridization.

-------

As for Iranics----a greater degree of such hybridization is more plausible simply given later definitive Iranic presence on the Western plateau than in NW India.

When it comes to material culture, it's hard to argue on the basis of BMAC vs Elamitic substrata because they seem to have been fundamentally similar and a preponderance of clearly Mesopotamian/Elamite motifs during Achaemenid era need not imply saltatory migrations. Trend adoption can be unidirectional between urban/semi-urban cultures.

In order to make better speculations on the basis of ADXMITURE results, I'll have to examine them again to gauge the nature of the cline and/or Iran_N/Iran_Chl ratios of West and East Iranics. From some cursory modeling I've done, though, things are unclear.

When I model Tajikistani groups in Dave's dataset, they get comparable amts of Iran_Chl and Iran_N in addition to their ~40% Sintashta-like and some (archaic?) ENA ancestry.
When I model modern other West Iranians on the other hand, they almost exclusively get Iran_Chl with the exception of the Mazandarani who take a good chunk of Iran_N, but not as much as, say, Yagnnobi do. (Again, this is in addition to their ~20% Sintashta/Andronovo-like.)

Let's suppose results obtained by other means agree. Would this indicate a jump across the Kavir? Not necessarily. As David implied, BMAC-related groups could have had highly variable Iran_Chl/Iran_N proportions. Perhaps groups associated with late Tepe Hissar/Gurgan Grey Ware were entirely Iran_Chl and these formed a significant substratum of the first Iranic-speaking settlers of Fars.

Btw, Iranics may not have been the first wave of steppe DNA bringers, either. I suspect Caucasus-crossing R1b groups with steppe ancestry and/or earlier Indo-Iranian speakers(Mitanni?) had limited presence in modern-day Azerbaijan region. If true, it complicates things further but it's tempting to think they didn't make a huge overall impact.

I gotta say---lot of this is like having a system of equations where there are more variables than equations but we've got rough range estimates for variables' values. Tantalizing af.

Anthro Survey said...

@MomOfZoha

I appreciate your compliments, mate.

Regarding the "Near Eastern" contribution---archaic CHG works best for modeling Yamnaya, iirc, and I suspect it will prove optimal in modeling that Eneolithic sample from Ukraine as well as future samples from earlier dates across the Sredny Stog horizon. That kinda rules out Dagestan/Azerbaijan hypothesis and accords more with a Western Caucasus and/or Colchis scenario.

We have a PRETTY good idea for our location(northern black sea), but the question is WHEN the earliest such populations---where individuals featuring comparable EHG and CHG proportions were typical---first arose. Certainly pre-Maykop, but between 5000 and 4500BC(as I suspect) or earlier?

The other question is that of the Shuvaleri-Shomu culture. Was this a product of strong demic influence from northern Messopotamia/east Anatolia carrying ANF-like ancestry? If so, we can kinda rule Colchis out as a source if my suspicions to the previous question hold. (There is clear craniometric evidence for such North Messopotamian influence in the S. Caucasus by 3500BC and even Maykop-era Adyghea, btw, not only material.)

And yes, for the most part, different ancestral clines/clusters spanning geographic zones were more meaningful millennia ago(or, say, pre-3000BC). Late Neolithic Moroccans, pre-dynastic Egyptians, Catalhoyuk dwellers(?) and Atlantic Megaliths shared a ton of drift and cultural features. This Old Euro-Mediterranean cline isn't very meaningful today regardless of the criteria set we choose, though, despite strong instance to the contrary by some Mediterranists prowling discussion boards on FB and elsewhere.

Wishing a happy holiday season to you as well!

Shahanshah of Persia said...

@Anthro Survey On a side note and sort of unrelated tangent, it would be interesting to see ancient Mesopotamian samples, and how closely they are genetically to modern Iraqis. Contrary to popular belief, I do not think that the Arabs had a significant impact, genetically speaking, on the Iraqi population. Unfortunately, in every study I have seen, all I have seen are Iraqi Jewish samples, not Iraqi Muslim samples (though, I have seen Assyrian samples as well). I personally feel that the Arab genetic impact on Iraq was limited, and not as much as it was on say, Syria or Egypt, because keep in mind, Iraq was always a source of opposition to the Umayyads, early on. The only known Arab settlements in Iraq were garrison cities in Kufa and Basra. In my opinion, these garrisons could in no way have outnumbered the total Iraqi population. There is evidence of later Bedouin settlement, but it was limited. Most likely, modern Iraqis are at the most, 20% Bedouin/Saudi derived. Most of their ancestry, especially that of Northern Iraqis, must come from the ancient Mesopotamians. Furthermore, aside from a bit of Subsaharan admixture (3 to 7% in Iraq), I hypothesize that modern Iraqis are between 75 and 90% similar to their ancestors. Now the only questions remaining are what kind of impact the Mongols had on changing the genetics of Iraqi, and how the Mongol invasion impacted Christian genetics in the region (i.e. Assyrians migrating north into Armenian lands). I would assume that most modern Iraqis are descended from rural agriculturalists, not the urban population of ancient Mesopotamia, as the Mongols devastated Mesopotamian urban centers, most notably, Baghdad. It may even be likely that modern Iraqis have little to no Arab contribution, because they are largely of rural stock, not of the cosmopolitan urban dwellers living in Mesopotamia for a millennia, any thoughts?

Seinundzeit said...

Anthro Survey,

Talk of saltatory migration brings to mind the Romani; they are a continuation of a migration rooted among the low-caste populations of North-Central India, so they obviously spent quite some time in West Asia.

Yet, despite the Near Eastern sojourn, I think that most analyses fail to detect much in the way of West Asian genetic ancestry (if I'm not mistaken, although I could be wrong); rather, they seem to be mostly North/Central Indian (of the "Scheduled Caste" variety) and Balkanite in terms of genetic ancestry.

So, your point about people migrating huge distances without picking up substantial admixture is totally sensible, even in the case of non-military expansions.

Davidski said...

@Shahanshah of Persia

I do not go full Davidski and speculate that the Achaemenids were almost entirely Steppe derived, as they would have had to pick up at least some admixture from Central Asia and Iran prior to coming to power.

Can't recall saying that, and it's not something that I think is very likely. Some of these individuals may have been almost fully steppe derived, but overall no.

@ Seinundzeit

Talk of saltatory migration brings to mind the Romani; they are a continuation of a migration rooted among the low-caste populations of North-Central India, so they obviously spent quite some time in West Asia.

Yet, despite the Near Eastern sojourn, I think that most analyses fail to detect much in the way of West Asian genetic ancestry (if I'm not mistaken, although I could be wrong).


European Romani do show recent West Asian ancestry.

Shahanshah of Persia said...

@Seinundzeit Good point, though, keep in mind that the Romani were always outcasts wherever they went, and thus could not as easily mix. Whereas Steppe raiders somewhat could and did. But overall, I do not think that the Indo-Aryans picked up much admixture in Central Asia, hence why isolate populations like the Kalash and Nuristani are to this day mostly Steppe derived. And according to Davidski, they do seem to show recent West Asian ancestry, interesting.

@Davidski Okay, thanks for clarifying. Sorry, I guess that was a poor assumption on my part then, I probably misread something you wrote. Anyway, I agree with what you have said here. On a side note, are there any pure Romani left today? And, are the Irish Travellers Romani or European? Thanks.

Matt said...

@Sein: In that context, "South_Indian" came out to be 50% Caucasus, 40% SE_Asian, and 10% Papuan

That does seems rather high as a % West Eurasian; comparing to the Reich ASI Estimate, which really does look 100% ENA, the Harappa South Indian spans about 15-20% of the distance between Iran_N, CHG, Steppe_EMBA (who are more towards the East Eurasian end of the main East-West PCA than more western counterparts).

Reich ASI tends to only be only 2-3% lower in many populations with ≈25% Harappa S Indian (Sindhi, Pakistan Pashtun, etc.), which would fit Harappa SI being about 0.8-0.85 of Reich's ASI as 0.15-0.2*0.25 about that sort of magnitude (0.5 would end up with populations who get in the range only having 13-15% Reich's ASI).

A simple f4 ratio or something probably would've told better how much it really had, I think (rather than processing back through ADMIXTURE components).

Thanks again and Happy Holidays.

Seinundzeit said...

David,

"European Romani do show recent West Asian ancestry."

Ah, so it seems that my memory wasn't serving me right; I just reread that old paper on Romani genetic history, and it looks like I had quite a few things wrong.

Would help if I had Global_10 PCA coordinates for Romani samples. Out of curiosity, do you have such samples?

Matt,

"That does seems rather high as a % West Eurasian; comparing to the Reich ASI Estimate, which really does look 100% ENA, the Harappa South Indian spans about 15-20% of the distance between Iran_N, CHG, Steppe_EMBA (who are more towards the East Eurasian end of the main East-West PCA than more western counterparts)."

True; but Reich's ASI estimates were likely to be somewhat off, as Near Eastern-related ancestry in South Central Asia + South Asia is of a very ANE-rich sort (Iran_N-related, and Iran_Chal for South Central Asia), and European-related ancestry in South Central Asia + South Asia is from sources far, far richer in ANE ancestry compared to all contemporary Europeans (perhaps Saami excepted; but they would still be terrible proxies, since they do have EEF-related ancestry, and 15%-25% ENA, depending on method).

For what it's worth, both qpGraph and qpAdm tend to show much lower ENA percentages (10%-15%).

With regard to the ADMIXTURE side of things, it's actually quite hard to get ENA levels to be in the Reich et al. range.

Zack's earlier K11, with a Iran_N-like West Eurasian component and a "Onge" component, only showed 11% ASI for Pakistani Pashtuns, 7% for the Balochi, and 5% for the Brahui.

In addition, when it comes to PCA data in conjunction with nMonte, one can only get South Central Asian populations to be 10%-15% Onge/Jarawa (referring to eigenvector scaled data; although one sees the same pattern even without scaling).

Finally, with my own ASI simulation for Fst-based PCoA (which, I should mention, has given me excellent results; prior to my use of it, South Central Asians and South Asians would get rather odd modelling, like lots of East_Scythian, and very little Iran_N for populations deep inside India. All those issues disappeared, which has given me some confidence), I also see a range of 7% to 17%, with my various Pashtun samples (I've been provided a bunch; they're from different tribal groups, and different parts of Afghanistan and Pakistan), around 15% with the Pakistani Pashtun samples, and 19% with the Sindhi (if my memory serves me right. Just to make sure, I'll check later).

Taking all of this into consideration, I think Everest's supervised ADMIXTURE run yielded sensible output.

(On a different note, the Baloch component was 97% Caucasus, 3% American! Nicely ties into the ANE theme)

Then again, ADMIXTURE components are abstractions (everything in historical population genetics is an abstraction with only a thin connection to non-statistical epistemic objectivity, but ADMIXTURE output takes this to a whole different level), and the presence of an ADMIXTURE component doesn't necessarily mean the same thing for the different populations in which it appears.

For example, Iran_N are 10% South_Indian with HarappaWorld, despite having 0% ASI.

"Thanks again and Happy Holidays."

Thank you!

Happy Holidays to you too! (Have fun)

Anthro Survey said...

@Shah

Variation with respect to more recent Arab ancestry in Iraq probably corresponds with geography, more than anything, when it comes to Muslims. Heavy Arab settlement did not become a thing in Mesopotamia until after 17th century or so, while in Anbar region it may have been the norm since antiquity. Anyway, those later settlements would have had their biggest impact in the southern regions of Iraq's fertile zone, iirc.

So, yes. Central and Northern Mesopotamian Iraqi Arab speakers should indeed, be reasonably good proxies for the ancient Babylonian populace. This is confirmed in their more "pan-MENA" phenotype: they overlap comfortably with Lebanese, Syrians, Armenians, West Iranians, and Anatolians. I can't say the same for a lot of southerners and Anbaris. Actually, the more fertile zones of the Levant would also remain relatively free of Arab introgression till about the same time period. Palestinian Muslims show the most variation/spread there, which probably corresponds to a greater degree of peninsular influence. As you might expect, they have quite a variation when it comes to looks. A good chunk pan pass seamlessly in places like Aleppo and Yerevan, but there are plenty of "desertic"---almost pseudo-SSA----types among them. To be sure, Lebanese Muslims seem to be more Natufian-shifted than their Christian counterparts but it's not so drastic.

Regarding SSA in Iraq and the ME in general---we should be cautious in taking that label at face value. "Actual" SSA ancestry is there, but is probably half or less of what is reported by these calculators. The rest of the score may instead correspond to a signal from a very basal ghost lineage that isn't well characterized. It's suspected by some to constitute a chunk of Bedouin as well as of Natufian and, even more so, early Neolithic Maghrebian ancestries. Harifian, Mushabian and pre-historic Egypt are other (yet unsampled) cultures suspected to have from this lineage.

If such a lineage existed, it would be:
1)an early back-migrant to Africa that then refluxed back to Eurasia circa 12000BC, mixing with Levantine locals and culminating in Mushabians, Harifians, Natufians and Circum-Arabian pastoral systems.
2)packed with and associated with spread of Y Hg E
3)ass. w/the spread of Afro-Asiatic languages

See this relevant tweet and responses. Doc Laz may be speaking too soon here:
https://twitter.com/iosif_lazaridis/status/910946340116541440

Anthro Survey said...

@Shah
To put things in more graphic perspective, these are my two hypotheses(mixing and its products not shown here to simplify things).

https://justpaste.it/1evdw
https://justpaste.it/1eve5

Shahanshah of Persia said...

@Anthro Survey I had a longer reply before the Mesopotamian one, but I don't think David liked it and he removed it. Unfortunately, :(.

Luckily for the both of us, I saved it! :) I save my replies, just in case.

Here, it's in two parts:

Part 1:

@Anthro Survey Yes, I definitely agree with your assessment here. Though, I would like to stress that I think the Iranics who entered Iran were at least 50% Steppe, and at the most 70% Steppe. I also think that the Achaemenid elite probably were between 40 and 60% Steppe derived, with a bit of admixture from Neolithic and Chalcolithic Iranians. The reason I say this is that we can see a similar phenomenon in India (which will hopefully be confirmed by the SWAT samples), whereby the Brahmin/Warrior castes are much more Steppe derived than the native populace. I would not be too surprised if we do get our hands on samples from members of the Achaemenid aristocracy in the near future, and this will probably confirm my speculations. I do not go full Davidski and speculate that the Achaemenids were almost entirely Steppe derived, as they would have had to pick up at least some admixture from Central Asia and Iran prior to coming to power. Though, what is probably true in my opinion is that both the Achaemenid and Parthian elites were heavily Steppe derived, as it is only with the Sassanids, where we begin seeing the elite carry similar levels of Steppe admixture to the general population (though, still a bit more Steppe derived). Even today, we can see this phenomenon in Iran, as Zoroastrians are the most Steppe derived, whereas some Iranic tribes are the least Steppe derived, Lurs being an example. As for the Indo-Aryans, I stand by my previous assessment that they were probably not very admixed by the time they reached India, just before establishing the Vedic era, and the SWAT samples shall confirm this, hopefully.

Shahanshah of Persia said...

@Anthro Survey

Part 2:

I think the Seljuks were already somewhat admixed in Central Asia with native Iranic tribes, but probably did not gain much admixture within Iran, prior to entering Anatolia. Though, the Seljuk elite probably did pick up some admixture later on when they began to Persianize themselves. In any event, the Seljuks in Anatolia probably only had admixture from Central Asian Iranic tribes, for the most part.

Yeah, I concur in regards to the point that they likely had to have some admixture from Central Asia. Though, I do not think that either the Vedic Aryans or early Iranics had significant non-Steppe admixture, and I would say that it was around 20%. But, probably not more than that. Now, whether or not the Vedic Aryans and early Iranics took a different route is a another question in itself. I would assume that perhaps the Iranics picked up more Chalcolithic Iran DNA and less Neolithic Iran DNA, whereas the Vedic Aryans probably picked up little to no Chalcolithic Iran DNA, and most of the non-Steppe admixture was likely from Neolithic Iranian farmers in the Ferghana valley.

Yes, overtime, there must have been a greater degree of hybridization, but it depends on when the Iranics actually arrived in Iran. That is the real point of contention here.

Yes, it's either one of the two, possibly both. Also, let's not forget the influence from the Yaz culture, which was probably mostly Chalcolithic Iranian early on, with it later being infiltrated and dominated by the Proto-Iranics, prior to their march into Iran.

Indeed, I definitely agree with your assessment of the results there. It would be interesting to see what BMAC peoples looked like, perhaps a mixture of Neolithic and Chalcolithic Iranians, most likely both. And you are right, later Iran Chalcolithic admixture must have been gained during their stay in Iran.

Yes, I do not think that the Iranics were the earliest, as it was most likely the Mitanni-Aryans. Mitanni-Aryans most likely resembled the SWAT Aryan samples, minus any ASI admixture.

It is indeed! Well, all we can do is wait for more DNA samples. Thanks again, I appreciate your reply.

I don't know why he deleted it.

@Davidski Please clarify what you didn't like.

Shahanshah of Persia said...

@Anthro Survey To get back to your latest reply, I definitely agree with you. Though, the SSA in North Africans is not due to a ghost effect. I think it's actual SSA. The reason I say this is because late Neolithic North African samples from Morocco barely showed any SSA at all, whereas modern North Africans have around 20%. There is no way that it could be due to Basal. In regards to other Middle Easterners, I do agree, I think half of what is picked up is Basal Eurasian, not actual SSA. Actual SSA in Arabia "proper" should be very limited due to the fact that most Black slaves were castrated and not aloud to mate with females. There is some maternal SSA in Hijazis, and I think it is legitimate, but in regards to Bedouins, Syrians, Iraqis, etc., I think half of it should indeed be basal. Though, most Christian Arabs lack this signal, I think most of it is actual, most likely. Though, it's not at all found in Iraqis to any significant degree.

On a side note, what's interesting is that it's the northern Iraqi Arabs who most likely resemble their ancestors more than any other Iraqi population. Which means that when those ISIS fighters destroyed the Assyrian/Babylonian reliefs and artifacts, most of them were, ironically, destroying what was built by their ancestors.

Thanks for sharing the tweet, it confirms my point that North Africans received actual SSA since the arrival of Islam, just as Egyptians did.

Thanks for sharing those graphics with me, much appreciated. I think the first one is more plausible than the second, by the way.



Nick N said...

Hi.

My Ancestry DNA results came back with a 47% British, 8% Scottish, 6% Scandinavian, 11% West Europe but what is surprising is the 16% Caucasus and 6% South Europe.

I have no known descendants from the Caucasus or South Europe. Is this % likely to be modern or ancient DNA ? Is there a way to work it out?

Baba Sa'azana said...

@ Davidski

So it can be described as a European population. Reasonable people without any agendas should be able to accept this without too much of a problem, no?

No offense but you're literally the only one here who seems to have an agenda... You're so fixated on them being "European" that you'll use silly arguments like how they share a lot of drift with modern Northern-Europeans as the reason why.

This is all plain-fact:

* Barely any population across Northern or Eastern Europe today even traces more than 50% of its ancestry to them. Not your own ethnic group, not Brits, not Swedes and Lithuanians or Latvians.

* 35-50% of their ancestry comes from the Middle-East/West-Asia (CHG).

* The remaining 50-65% of their ancestry traces a significant proportion of its ancestry to Upper-Paleolithic Siberia (ANE).

* Not a single group like ethnic Russians, Poles, Swedes or what have you overlaps with the Yamnaya due to their significant Anatolian-Neolithic and peninsular WHG ancestry which, news flash, tends to basally make up more of their ancestry than Yamnaya-related ancestry does.

Yamnaya-related people were integral to the creation of modern European genetic variation but they clearly exist outside of it as simply a contributing force like Neolithic-Anatolians who, inconveniently for you, didn't geographically form in what is now "Europe" or you'd be designating them as "European" as well I reckon.

You're just obsessed with emphasizing that they're "European" because you have some strange obsession with being as native to the region as possible, evidenced by how you used to display glee at how "Hunter-Gatherer" Northern Europeans like Poles seemed (in comparison to "EEF") even back around 2013 when we were mainly still on the ANE+EEF+WHG model from the Lazaridis et al. paper from back then.

And this map has to be one of the silliest things I've ever seen:

https://drive.google.com/file/d/0B9o3EYTdM8lQelZhUGYtN1g1VnM/view

The actual line should be between WHGs&EHGs Vs. the various pre-historic Middle-Eastern groups like CHG+Iran_N and Natufian+Levant_N+Anatolia_N. Why? Because, you of all people know full-well that there hasn't been much of a rigid divide between Europe and "Asia" since the bloody Neolithic. And Rob is right, the only truly native ancient "European" group are perhaps WHGs. Every other group, EHGs included, are either UP-Siberian or Epipaleolithic~Neolithic Middle-Eastern admixed or both and the Early Bronze Age Steppe groups, as pointed out earlier, were sure as shit not safe from this.

But keep screaming at the top of your lungs that they were "European" using whatever silly semantic arguments you have. You just display how biased and chauvinistic you are and just why you're no actual scholar who's been taught to remain objective. You're competent with all these analyses but otherwise...

Davidski said...

@Baba Sa'azana

Archaeological cultures like Sredny Stog and Yamnaya formed and were located in Eastern Europe.

It's very basic geography. So don't over think this, just look at a decent map...

Map of ancient Central and Eastern Europe

Obviously, there's a reason why the map above is not a map of Central or even West Asia. Quit being so butt hurt and focus more on your own heritage and origins.

Nothing more to add.

Baba Sa'azana said...

Amazing rebuttal, you didn't even refute anything I said. But I suppose because their genetic structure would have likely formed in Africa IAM and Keb are "African"? You're just oversimplifying things to suit your needs.

Yamnaya-related people are largely the result of intermixing between Eastern-European Hunter-Gatherers (themselves part UP-Siberian) and West-Asians carrying significant CHG-related ancestry. They don't fit in the variation of modern Europeans either genetically or phenotypically, it is disingenuous to group them with modern Europeans as a result simply due to semantics like geography these bronze age people wouldn't have cared about. They are their own entity entirely but contributed a lot to modern Europeans (particularly Northern ones) who wouldn't exist without them.

It's not complicated and you're smart enough to get it. ;-) I have nothing to add as well. Good day to you.

Shahanshah of Persia said...

@Baba Sa'azana

Well, the Yamnaya people are closer to Europeans than any other people, and they originated in Europe as well, despite being partially West Asian. Anyway, why don't you focus on your own heritage and your half-African and half-Natufian origins? It's not like the Yamnaya came from Africa, now is it? They were a Caucasoid people, not a Negroid-Caucasoid (Semitic) hybrid, such as yourself. Concentrate on your own roots.

Baba Sa'azana said...

First off, don't assume people's origins. I have a thing for Haile Selassie's look and like Semitic type names like "Sa'azana" (Ge'ez name) but I'm a Flem from Belgium in actuality = these people are as part of my heritage as Davidski's.

Now, if you're done cuckolding yourself for Europeans like us who see you as a sand-negro regardless, you should take a moment and realize how foolish you are for also using semantic arguments like "They are closest to Europeans" to argue that they are "European". Everything I wrote earlier is not hard to understand, Shahanshah. Read it and move on.

Concentrate on your own roots.

The sheer hilarity of this is palpable. You're demonstrating exactly what I meant when I said Davidski proves that he is not any scholar who has been taught to remain objective. You share the same traits. You both seem to completely lack a genuine, scholarly curiosity in these things hence your inability to fathom that someone not from a region (I am from the region, however) would be interested in the history, linguistics or genetics of that region. You know, simply cos they genuinely like all this anthropology stuff and aren't looking to spread some agenda about their own people. Is it a crime for a Dutchman like me to take an interest in Arabian or Ethiopian history or Chinese history? You people are such a joke that you can't even try to seem like you have a sincere interest in the field... :-)

Now, this'll be my final reply. Take care of yourself.

Davidski said...

@Baba Sa'azana

Everything I wrote earlier is not hard to understand.

It is, because you're not making any sense, to the point that I had to simply ignore all of your ramblings.

Just to give you one example: you accept that Europe is a modern-day concept, and yet at the same time you claim that WHG is the only real European population.

Obviously, if Europe is a modern-day concept, it's defined by modern-day continental borders and peoples, in other words modern Europeans. So in fact, strictly speaking, WHG is not really a European population, because it's outside range of modern-day European variation.

However, Bronze Age peoples from the western steppe cluster more or less within the range of modern-day Eastern European variation, so not only are their burials located geographically within what is now Eastern Europe, but they cluster with modern-day Eastern Europeans.

So what are they then? Duh? Obviously Eastern Europeans.

These people are as part of my heritage as Davidski's.

You can't ignore the geography in this discussion, because it's mostly about geography. So no, not unless Belgium is in Eastern Europe, which obviously it isn't.

Shahanshah of Persia said...

"First off, don't assume people's origins. I have a thing for Haile Selassie's look and like Semitic type names like "Sa'azana" (Ge'ez name) but I'm a Flem from Belgium in actuality = these people are as part of my heritage as Davidski's."

I know it's a Ge'ez name, and I also know who Selassie is. In case you did not know, Ethiopians are half Semitic. Anyway, you should have known this by now.

"Now, if you're done cuckolding yourself for Europeans like us who see you as a sand-negro regardless, you should take a moment and realize how foolish you are for also using semantic arguments like "They are closest to Europeans" to argue that they are "European". Everything I wrote earlier is not hard to understand, Shahanshah. Read it and move on."

David has never called me a sand-negro. No one here has, and just because a few people are ignorant, it does not mean that everyone is. You are the one cuckolding here, not me. You are cuckolding for people who you want to be accepted as your kind. You are a cuck! Anyway, I am not going to bother arguing with you, just look at David's reply.

"The sheer hilarity of this is palpable. You're demonstrating exactly what I meant when I said Davidski proves that he is not any scholar who has been taught to remain objective. You share the same traits. You both seem to completely lack a genuine, scholarly curiosity in these things hence your inability to fathom that someone not from a region (I am from the region, however) would be interested in the history, linguistics or genetics of that region. You know, simply cos they genuinely like all this anthropology stuff and aren't looking to spread some agenda about their own people. Is it a crime for a Dutchman like me to take an interest in Arabian or Ethiopian history or Chinese history? You people are such a joke that you can't even try to seem like you have a sincere interest in the field... :-)"

No one said it's a crime or anything. But sometimes people like you would rather believe the Cultural Marxist's narrative. Everyone has an agenda, I thought you would know this by now. It's not like we're the only ones with "agendas". It's not about sincere interest. If you do not like what we are saying, perhaps you would be satisfied on a Afrocentrist or Islamocentrist forum.

"Now, this'll be my final reply. Take care of yourself."

Same, good day to you.

@Davidski

"It is, because you're not making any sense, to the point that I had to simply ignore all of your ramblings."

A bit loony he is, if you ask me. Hence, why it's best not to comment. It will just lead to a worthless argument.

"However, Bronze Age peoples from the western steppe cluster more or less within the range of modern-day Eastern European variation, so not only are their burials located geographically within what is now Eastern Europe, but they cluster with modern-day Eastern Europeans.

So what are they then? Duh? Obviously Eastern Europeans."

Well said, David! Well said.

"You can't ignore the geography in this discussion, because it's mostly about geography. So no, not unless Belgium is in Eastern Europe, which obviously it isn't."

Indeed, it is not.

Anthro Survey said...

@Shah

That is a reasonable assumption on your part and I, too, believe that early Median and Achamenid nobility had elevated steppe ancestry compared to the general population---perhaps in the neighborhood of 40%.

I speculate that such a scenario probably held for CeltIberian early Italic(Umbro-Samnite) nobilities. In the former case, we can assume they were NorthernFrench-like, 2D PCA-wise. In the latter case, they packed more steppe ancestry, less Bronze Age Anatolian input and likely sported individuals resembling Ignazio Abate. I'd also say their Anatoalian:EEF ratio was lower, too, since I take Anatolia_BA-like ancestry to have been stronger in the lowlands, not Apennines.

IIRC, Mazandaranis pack the most steppe in modern Iran from the sampled populations, but I suspect locals(as opposed to resettled Kurds) in Nishapur and Masshad pack even more. Zoroastrians pack more of it compared to the people they live among, though.

Re/Seljuks---
Ofc, I am sure they had assimilated Sarmatians, Scythians west of the Urals. How else would Karalpaks or Kazakhs get R1a, yamnaya signal and "Turanid" as opposed to "Mongoloid" looks? It's possible that those Scythians "taught" the early Turkics the way of the horse(incl. archery) only to end up on the receiving end of a cruel irony. The dynamics of processes on the eastern steppe, particularly in regards to Uralic and Turkic expansions, will be elucidated in the future with Seima-Turbino DNA. Turkics probably assimilated R1b-rich Afanasievo offshoots, too, hence the R1b in Turkmenistan(perhaps they were assimilated previously by Scythians).

Anyway, I was referring to the sedentary, urban Iranic-speaking peoples of the Oxus and Mughrab regions. From what we can tell, minimal mixing took place between them and pre-Islamic Turks, who were occasional overlords in the area. Minimal mixing took place during Seljuk times. Mixing intensified after the 1500s and was bi-directional. That's why Uzbeks have a strong BMAC signal, while Tajiks get a non-negligible ENA signal.


"most of the non-Steppe admixture was likely from Neolithic Iranian farmers in the Ferghana valley"

That or maybe the Iranian farmers of Bactria were more Iran_N-like than those of Margiana. Clines....

Anthro Survey said...

West of the ALTAI, not Ural, I mean.

Anthro Survey said...

@Shah

Regarding SSA---

Once again, I am not denying the presence of REAL SSA admixture in contemporary North Africa and Near East(mainly in Muslims). It is certainly there as evidenced by formal stat results, but probably does not account for the entirety of the SSA signal.

Arabophone Maghrebis likely pack 10% REAL SSA admixture, while the other 10% is owed to some Natufian/IAM-specific admixture lacking in other basal-rich populations. Berbers of the Rif and Kabyle, on the other hand, probably get little real SSA and owe most of their "SSA" on calcs to that TBD ancestry. Berber results resemble those of the Guanche, more or less, if you've looked at that paper.

That PCA does not CONFIRM, per se, but shows results CONSISTENT with SSA introgression. 2D PCA has a limited projection capability and a shift towards SSAs(as is the case with Natufians and IAM) needn't imply real SSA phylogeny. Hence, I said Lazaridis jumped to the hasty conclusion that it had "re-increased" and the comments in that thread echo my opinion.

Matt said...

@Sein, hmm, I'm not totally confident in the patterns using Onge and Jarawa components in PCA/ADMIXTURE because of the likelihood that these have some different drift going on which makes them less attractive as clusters for either the SA component or real SA populations.

But yeah, actually thinking about it, on your other point, Reich's f4 ratio could be a little off from EHG / Iran_N having more ENA like ancestry than their Basque and Georgian proxies in the ratio I guess (through Ancient North Eurasian having more ENA like ancestry deep in the mix than equivalents further west?) and the divergences between ancient non-ENA ancestries.

Also, may be of interest but since coming back from hols I repeated the exercise from Eurogenes K13 above with the Harappa Project K15 spreadsheet.

So this is using PCoA Fst to create dimensions capturing distance between components, then projecting populations on to them based purely on the 5 broadly West Eurasian components (Baloch, Mediterranean, Caucasian, NE Euro, SW Asian) and running analyses.

This is kind of interesting to me as Zack Ajmal's database is really so much richer in South Central Asian populations than any other project.

So: https://imgur.com/a/8jVNI and https://ibb.co/nLD29w / https://ibb.co/cqWdhG and https://ibb.co/fmftGb

(Again, this is based purely on the WE components, after masking out the broadly non-WE components to the best of my ability: S Indian, Baloch, Caucasian, NE Euro, SE Asian, Siberian, NE Asian, Papuan, American, Beringian, Mediterranean, SW Asian, San, E African, Pygmy, W African. (S Indian is hard to call, as we've discussed as either of these categories.)

So if you see in the above link that African American clusters with British or Puerto Rican with Spanish, for instance, this actually means something like "The West Eurasian component ancestry in African Americans clusters closest to British", which does kind of make historical sense).

There's not a huge amount of variation in the S Asian populations (populations with high S Indian) as they mostly all take large amounts of Baloch component. It's not as stark as with the Eurogenes K13. But there is a pretty interesting substructure at the margins where South Indian populations clearly tend to in cline relatively more to the kinds of SW Asian linked South Asian ancestry found in the Brahui-Makrani-Balochi group, as well as having more Baloch component. Caste has a strong role, but it is also the case that the position of the Kerala Brahmin and Rajasthani Brahmin are immediately different within the general cline in the context of the WE portion of ancestry. Structure is also pretty geographical with North-South and East-West structure, after partialling out S Indian.

(Note, the Singapore Indian D sample gets an unusual position in the above. It is a sample with N=1, so one person and I would guess he or she probably has an unusual Anglo-Indian ancestry. Hence the unusual high level of NE Euro component.)

This is really at the margin though. From this, seems almost no Fst between the West Eurasian parts of even extreme populations on the above (e.g. West Eurasian part of Tamil Nadu Scheduled Caste vs West Eurasian part of Rajasthani Jatt would have predicted Fst of 0.005 while WE TN Brahmin vs WE TN Dalit 0.001).

Still probably a lot more potential in Zack's database to analyse the substructure in different W Eurasian related ancestries in India, if it's combined with ancient dna, since he has really good geographical coverage. Other sets seem to have gone for extremes on the ANI-ASI scale (e.g. mainly Pakistan and Brahmin in the north and mainly tribal populations in the south) at the expense of the broad middle who have more pronounced differences in their broadly West Eurasian type ancestry.

(Few more graphics with no masking: https://ibb.co/etYSsG, https://ibb.co/j07Rmb, https://ibb.co/bGOMKw, https://ibb.co/cM8csG, https://ibb.co/j5SsRb)

Shahanshah of Persia said...

@Anthro Survey

Sorry for the late reply, I have been very busy.

"That is a reasonable assumption on your part and I, too, believe that early Median and Achamenid nobility had elevated steppe ancestry compared to the general population---perhaps in the neighborhood of 40%."

I personally think that it was a bit higher than that, up to 60%, perhaps even as high as 70%.

"Arabophone Maghrebis likely pack 10% REAL SSA admixture, while the other 10% is owed to some Natufian/IAM-specific admixture lacking in other basal-rich populations. Berbers of the Rif and Kabyle, on the other hand, probably get little real SSA and owe most of their "SSA" on calcs to that TBD ancestry. Berber results resemble those of the Guanche, more or less, if you've looked at that paper."

I do not think that this is the case. I feel that it is around 20%. However, you could be right, perhaps. I did, but Guanche had around 10% SSA on average, so I think that's what you mean. Perhaps the SSA is due to Basal admixture, though, other possibilities cannot be counted out either.

"That PCA does not CONFIRM, per se, but shows results CONSISTENT with SSA introgression. 2D PCA has a limited projection capability and a shift towards SSAs(as is the case with Natufians and IAM) needn't imply real SSA phylogeny. Hence, I said Lazaridis jumped to the hasty conclusion that it had "re-increased" and the comments in that thread echo my opinion."

I do not think that it was a hasty conclusion, but that's just me. Perhaps, it was, who knows?

Shahanshah of Persia said...

@Anthro Survey

"I speculate that such a scenario probably held for CeltIberian early Italic(Umbro-Samnite) nobilities. In the former case, we can assume they were NorthernFrench-like, 2D PCA-wise. In the latter case, they packed more steppe ancestry, less Bronze Age Anatolian input and likely sported individuals resembling Ignazio Abate. I'd also say their Anatoalian:EEF ratio was lower, too, since I take Anatolia_BA-like ancestry to have been stronger in the lowlands, not Apennines."

I think the Latin elites probably even had more Steppe, and I sort of agree with your analysis here in regards to the early Italic elites.

"IIRC, Mazandaranis pack the most steppe in modern Iran from the sampled populations, but I suspect locals(as opposed to resettled Kurds) in Nishapur and Masshad pack even more. Zoroastrians pack more of it compared to the people they live among, though."

Yes, this is most certainly true.

"Re/Seljuks---
Ofc, I am sure they had assimilated Sarmatians, Scythians west of the Urals. How else would Karalpaks or Kazakhs get R1a, yamnaya signal and "Turanid" as opposed to "Mongoloid" looks? It's possible that those Scythians "taught" the early Turkics the way of the horse(incl. archery) only to end up on the receiving end of a cruel irony. The dynamics of processes on the eastern steppe, particularly in regards to Uralic and Turkic expansions, will be elucidated in the future with Seima-Turbino DNA. Turkics probably assimilated R1b-rich Afanasievo offshoots, too, hence the R1b in Turkmenistan(perhaps they were assimilated previously by Scythians)."

Interesting observations. You are probably correct in your analysis here, mate.

"Anyway, I was referring to the sedentary, urban Iranic-speaking peoples of the Oxus and Mughrab regions. From what we can tell, minimal mixing took place between them and pre-Islamic Turks, who were occasional overlords in the area. Minimal mixing took place during Seljuk times. Mixing intensified after the 1500s and was bi-directional. That's why Uzbeks have a strong BMAC signal, while Tajiks get a non-negligible ENA signal."

Wait, so there might have been pure Eastern Iranics living in Central Asia until the 1500s? You could indeed be right here, considering that most Uzbeks and Turkmen have a great deal of West Eurasian Y-DNA, and this likely suggests assimilation as opposed to mass rape and conquest.

"That or maybe the Iranian farmers of Bactria were more Iran_N-like than those of Margiana. Clines...."

Perhaps, but who knows? The upcoming study will reveal the realities my friend.

Matt said...

@Sein, banging on again here a bit, but btw, re: "Zack's earlier K11, with a Iran_N-like West Eurasian component and a "Onge" component, only showed 11% ASI for Pakistani Pashtuns, 7% for the Balochi, and 5% for the Brahui", I had a quick look at this using the reference data and Fst data from here: http://www.harappadna.org/2011/04/reference-3-admixture-k11/.

The K11 S Asian component actually doesn't look too Iran_N like to me. See here for where I would project it to plot based on Fst+PCoA and reprocessing that with PCA: https://imgur.com/a/5svYs. It looks like a component that already bears some S Asian specific ENA related genetic drift. Not so much Iran_N - Iran_N is displaced away from S Asia and E Asia towards the Near East in ways that require admixture from more northern components and an ENA population to fit models. The K11 S Asian component mostly overlaps present day northern S Asia in the basic ENA-West Eurasia contrast, but at a slight remove that requires admixture from Onge / Europeans to model most S Asian pops precisely. Distribution of K11 S Asian also does not peak so much with what we'd expect Iran_N to but in Indians from North India, and with Kalash...

Likewise when Zack projected a zombie of it on PCA: http://www.harappadna.org/2011/05/indian-cline-iii/

The K12 run in the same above spreadsheet where Onge is very specific and only 1% in Pathan, has a S Asian component that looks (per Zack's zombie PCA above) to fit as a more purely ASI component and there is 26% in his Pathan sample (e.g. same as in Reich's estimate). (Other problems with this run though - Kalash component).

Also remembered that while I said "Reich's f4 ratio could be a little off from EHG / Iran_N having more ENA like ancestry", David's AdmixtureGraph using Steppe_EMBA and CHG and Iran_N still showed 19% ENA in Kalash, so actually likely not off that much.

Then I'd say about 20% ENA-ASI is probably still a good bet for populations from Pakistan given above.

Seinundzeit said...

Matt,

"The K11 S Asian component actually doesn't look too Iran_N like to me."

Considering that we're referring to an ADMIXTURE component, we must admit that, at a certain point, one becomes entangled in the fallacy of misplaced concreteness.

"Distribution of K11 S Asian also does not peak so much with what we'd expect Iran_N to but in Indians from North India, and with Kalash."

I did make mention of a broader ontological issue, right above; but with that being said, I should now also make mention of the fact that Iran_N/Iran_Hotu-related ancestry does seem to peak in contemporary North Indians and the Kalasha.

To be a bit more precise, the Brahui and Baloch have a rather decent amount of Iran_Chal-related affinity, while the Near Eastern ancestry seen in North Indians seems to be significantly skewed towards Iran_N/Iran_Hotu (to a lesser extent, the same holds for the Kalasha).

"David's AdmixtureGraph using Steppe_EMBA and CHG and Iran_N still showed 19% ENA in Kalash, so actually likely not off that much..."

True, I think it did show 18%; but for what it's worth, only in the joint-fitting topologies. When only including the Kalash, he found 10% ASI.

I think this is important to note, because the topologies involving only single South Central Asian and South Asian populations were much more sensible in a few other ways. For example, their demonstration of differential streams of West Eurasian-related ancestry, which was in great contrast to the co-fitting topologies (the co-fitting topologies almost always posited a unitary ANI phenomenon).

The former notion (multiple/independent streams of West Eurasian ancestry) is going to be validated by upcoming aDNA. So, taking into consideration the brute fact of the thing (reality of aDNA vs modelling), I think we are forced to put much less stock in the co-fitting topologies.

Also, 10%-15% ASI is what one sees with other methods, both formal (David's latest qpAdm runs) and PCA/ADMIXTURE-based.

"Then I'd say about 20% ENA-ASI is probably still a good bet for populations from Pakistan given above."

I think 20% ASI is an underestimate for most Pakistanis.

The average Pakistani is of Punjabi heritage, and they are (on average) probably around 30% ASI, but with a range of 20% to 40%, depending on caste/"biraderi", geography, and a few other factors.

To go totally cookie-cutter on my part, when looking at Pakistan, it's probably reasonable to say that in Balochistan, the Pashtun highlands, and in the Dardic highlands, people will vary between 5% and 15% ASI. By contrast, in the portion of Pakistan traditionally tied to Greater India/South Asia proper, one will see a range of 15% to 40% ASI, depending on caste, geography, and proportion of non-South Asian ancestry (e.g., things like recent Pashtun heritage, recent Baloch heritage, or an older Turkic infusion, or even distant Persian antecedents).

To be continued...

Seinundzeit said...

Continuing from where we left off...

But even after factoring all of this into our general picture, the whole model of West Eurasian vs ASI is probably not quite effective at describing reality as it truly is, since Iran_N/CHG and ANE/EHG already had substantial ENA ancestry (prior to their entrance into the Central/South Asian scene).

In fact, even WHG and Anatolia_N seem to be affected by a stream of ENA ancestry. Which is why Reich and Lipson, in their most recent thinking (as per my last conversation with them), are of the view that contemporary Western Europeans are probably around 20% ENA.

In terms of simple fact, the only West Eurasians bereft of ENA admixture are probably UP Europeans like Kostenki14, and perhaps the Natufians.

Looking at the big picture, West Eurasians themselves aren't an objective phylogenetic unit, unlike East Asians, considering that we represent the melding of extremely divergent Basal Eurasians with two highly distinct/distantly related eastern and western groups, but with the addition of widespread ENA ancestry (not to mention some highly divergent African admixture in the Near East/Northern Africa). But, we do share lots of drift, and lineages, courtesy of expansions that occurred during the Neolithic and Bronze Ages; that's about it.

So again, in a deeper sense, the Iran_N vs ENA distinction is (to a certain extent) a matter of analytic convenience. We utilize these distinctions for the sake of pragmatic worth/ease of analysis, even though the distinctions aren't wholly in-tune with the phylogenetic reality.

This was just a little tangent on my part; I like thinking about the bigger picture.

Hopefully, we'll see some aDNA in 2018 that'll add more flesh to our general conception of deep genetic ancestry for contemporary populations.

On that note:

Happy New Year!

Have fun, and stay safe! (Don't get too drunk! Lol)

Seinundzeit said...

Matt,

Oh, before I go to wreck havoc on the streets (lol), I should mention this:

https://www.biorxiv.org/content/early/2017/12/29/240812

I'd like to hear your opinions concerning this method.

(We'll talk after New Year's day; or, at the very least, before the end of January)

Matt said...

Sein: True, I think it did show 18%; but for what it's worth, only in the joint-fitting topologies. When only including the Kalash, he found 10% ASI.

Good point. Potentially though for non-cofitting models, I do think qpGraph can "slide around" a bit under these models and end up with ancestor populations with similar positions in nodes but which are a bit different in the actual drift path, which is still one problem that nags at me for these qpAdm methods with high numbers of ghost populations.

(the co-fitting topologies almost always posited a unitary ANI phenomenon)

The former notion (multiple/independent streams of West Eurasian ancestry) is going to be validated by upcoming aDNA.


Though the cofitting models I'm thinking of did not involve a unitary ANI, exactly, in the sense that the Iran_N and Steppe_EMBA were still separate nodes contributing to separate ANI, but the Iran_N and Steppe_EMBA were the same for all population, and ASI. The constraint is towards using the same Iran_N / Steppe_EMBA, etc. rather than the single fitting models that allow them to vary and shift the drift path that leads to each.

Unitary or structured in the tree model made no difference in the cofitting model: https://imgur.com/a/liYZI

Could still be in some way there really is a greater unity to the "ANI" in the way suggested by some of the the ADMIXTURE results, with separate streams of ancestry being somewhere between the idea of total unity and descent totally from structured steppe / Iran_N like populations, and the qpGraph is trying to cope with that? I really don't know.

Looking at the big picture, West Eurasians themselves aren't an objective phylogenetic unit, unlike East Asians

Yeah, I mean, it looks like the ancestry of groups from West Eurasia derives from a bunch of populations who split off at varying points on a tree out of the bottleneck out of Africa, and some members may be within the clade of ENA.

Think ENA is a pretty deep clade with lots of merging within to get present day populations. Tianyuan suggests this. Present East Eurasian heterozygosity (seems comparable to EEF) looks be difficult to explain otherwise, given all ancient dna so far shows groups living in small structured clades with low heterozygosity (even in Near East with admixture from divergent BEu and other clades), unless East Eurasia an exception to this. But certainly ancestors of East Eurasians "more" of a single clade, though lots of admixture within clade and high time depth of structure in that clade (maybe higher and deeper than in the UP European clade based on Tianyuan).

Matt said...

Sein: I'd like to hear your opinions concerning this method.

Honestly, I feel I have nothing of value to say there. I can't really say I'm certain I have a grasp the fine details of how the method actually differs in operation to the ADMIXTURE. I understand that they are estimating a space, then estimating ancestors and proportions from the limits of that space, and constraints? I think?

I can interpret the Figure 4b which shows that under difficult conditions where you have only a narrow cline of present day populations who are far from the trues edges (ancestors). They state "Both Admixture and ALStructure provide solutions qualitatively similar to the truth. While the points in the Admixture solution extend much further along the edge of the simplex than the true model, the ALStructure solution spreads into the interior of the simplex more than the true model."

That is maybe somewhat like some of the clines we are interested in? South Asian cline. Though in that case there is more dimensionality from Austro-Asiatic populations, etc. Applied to that cline ADMIXTURE might fit populations closer to the edge (e.g. ancestors) while ALStructure solution fit them further than reality.

Fig 6 shows that ALStructure is still pretty unable to recover the subtle population structure particularly in its last example, where there is subtle, continuous, spatial population structuring.

Fig 7 seems to show that the first two rows of Q are different for each algorithm - under the classic ADMIXTURE, they seem more conditioned by most distant populations in datasets, under ALSTRUCTURE more by the bulk of populations within the dataset. (E.g. compare how they look under the Human Origins panel).

Overall, the accuracy gains don't present but low, and there are speed gains over using ADMIXTURE.

Nathan said...

@Shahanshah of Persia
"Indian Nationalists" can be a misleading term. I am Dravdian; these Indians pushing O.I.T / Hindutva revisionism are mostly upper caste Hindus from North India and Brahmins from South India. These upper castes identify as Aryan, so they want to claim IVC is Aryan and Aryans are native. It is no different to White Supremacists claiming Ancient Egypt and Sumer were created by Whites and Whites were the first people in the Americas.

Nathan said...

@Jijnasu

"While there were very likely migration of Indo-Aryans into the subcontinent in the bronze age, one can't help but notice that an element of racism and euro-centrism continues to colour views on the issue. If the facts were all that mattered one would hardly stress on the 'europeanness' of yamnayans (a highly anachronistic and arbitrary term)"

The irony Jijnasu is that O.I.T and the Indian/Hindutva Nationalist version of history is steeped in racism, of the Aryan supremacy type, because Hindu Nationalists from the upper castes want to deny they ripped off a lot of pre-Aryan culture and they want to deny pre-Aryan peoples created the Indus Valley Civilization. Like White Supremacists trying to claim the civilizations of other peoples, these Hindu Aryan Supremacists want to claim the Indus Civilization for the glory of the Aryans.

South Asia is very racist and this comes from its caste system. The upper castes who identify as Aryan wants everyone to believe their Aryan ancestors were the creators of civilization and the dark skinned masses were inferior backward people. In this way they identical to pre-War European historians who tended to credit Indian civilization to Aryans.

Anthro Survey said...

@Shah

"Wait, so there might have been pure Eastern Iranics living in Central Asia until the 1500s?"

Yup, I'm sure Turkic admixture did not become a regularity in the Tajik classes well after the Mongol invasions.

Again, the reason I think Laz came to a hasty conclusion is because he'd assumed that IAMs' SSA admixture is what pulls them in that general directions on the PCA in the first place. The uniparentals from that paper make such a scenario unlikely, at best. Besides, Natufians behave in a similar fashion despite them not sharing more alleles with SSAs than, say, WHGs do.
Notice also that IAMs pull at a slight angle compared to contemporary Maghrebis(who doubtlessly have actual SSA).

It actually makes sense if you can picture some phylogeny.An archaic component population ancestral to IAMs sitting close to some basal MRCA for Eurasians should appear to be pulled towards SSAs compared to contemporary Eurasians in a 2D world PCA. Considerably shorter drift distance.

Who knows? A basal lineage----more basal to that which is pre-eminent in most Near Eastern peoples---could deff be the culprit. I stress "most" here, because Egyptians and Bedouins(most direct Harifian/Circum-Arabian heirs?) could harbor a lot of it.
If it turns out to be so, I suspect some calculators will need serious re-calibration.

Unknown said...

This is what Underhill had to say in his paper (from which the picture at the top was sourced):

Although the R1a1a* frequency and diversity is highest among Indo-Aryan and Dravidian speakers, the subhaplogroup R1a1a7-M458 frequency peaks among Slavic and Finno-Ugric peoples. Although this distinction by geography is not directly informative about the internal divisions of these separate language families, it might bear some significance for assessing dispersal models that have been proposed to explain the spread of Indo-Aryan languages in South Asia as it would exclude any significant patrilineal gene flow from East Europe to Asia, at least since the mid-Holocene period.